5V2C | pdb_00005v2c

RE-REFINEMENT OF CRYSTAL STRUCTURE OF PHOTOSYSTEM II COMPLEX

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.163 (Depositor), 0.160 (DCC) 
  • R-Value Work: 
    0.092 (Depositor), 0.090 (DCC) 
  • R-Value Observed: 
    0.095 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 3.0 of the entry. See complete history. 

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 3ARC


Literature

Chlorophyll a with a farnesyl tail in thermophilic cyanobacteria.

Wiwczar, J.M., LaFountain, A.M., Wang, J., Frank, H.A., Brudvig, G.W.

(2017) Photosynth Res 134: 175-182

  • DOI: https://doi.org/10.1007/s11120-017-0425-4
  • Primary Citation of Related Structures:  
    5V2C

  • PubMed Abstract: 

    Photosystem II (PSII) of oxygenic photosynthetic organisms normally contains exclusively chlorophyll a (Chl a) as its major light-harvesting pigment. Chl a canonically consists of the chlorin headgroup with a 20-carbon, 4-isoprene unit, phytyl tail. We have examined the 1.9 Å crystal structure of PSII from thermophilic cyanobacteria reported by Shen and coworkers in 2012 (PDB accession of 3ARC/3WU2). A newly refined electron density map from this structure, presented here, reveals that some assignments of the cofactors may be different from those modeled in the 3ARC/3WU2 structure, including a specific Chl a that appears to have a truncated tail by one isoprene unit. We provide experimental evidence using high-performance liquid chromatography and mass spectrometry for a small population of Chl a esterified to a 15-carbon farnesyl tail in PSII of thermophilic cyanobacteria.

    • Organizational Affiliation: 
    • Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520-8107, USA.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II protein D1A,
T [auth a]		344Thermostichus vulcanusMutation(s): 0 
EC: 1.10.3.9
Membrane Entity: Yes 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II CP47 reaction center proteinB,
U [auth b]		506Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II CP43 reaction center proteinC,
V [auth c]		458Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II D2 proteinD,
W [auth d]		342Thermostichus vulcanusMutation(s): 0 
EC: 1.10.3.9
Membrane Entity: Yes 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit alphaE,
X [auth e]		83Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit betaF,
Y [auth f]		44Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein HG [auth H],
Z [auth h]		65Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein IAA [auth i],
H [auth I]		38Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein JBA [auth j],
I [auth J]		40Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein KCA [auth k],
J [auth K]		37Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein LDA [auth l],
K [auth L]		37Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein MEA [auth m],
L [auth M]		36Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II manganese-stabilizing polypeptideFA [auth o],
M [auth O]		245Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein TGA [auth t],
N [auth T]		32Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II 12 kDa extrinsic proteinHA [auth u],
O [auth U]		104Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c-550IA [auth v],
P [auth V]		137Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein Ycf12JA [auth y],
Q [auth Y]		30Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein XKA [auth x],
R [auth X]		41Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein ZLA [auth z],
S [auth Z]		62Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
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Small Molecules
Ligands 26 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD
Query on DGD
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AN [auth c]
BN [auth c]
GE [auth C]
GP [auth h]
HE [auth C]
AN [auth c],
BN [auth c],
GE [auth C],
GP [auth h],
HE [auth C],
HO [auth d],
IE [auth C],
OF [auth D],
TG [auth H],
ZM [auth c]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CLA
Query on CLA
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AC [auth B]
AE [auth C]
AL [auth b]
BC [auth B]
BE [auth C]
AC [auth B],
AE [auth C],
AL [auth b],
BC [auth B],
BE [auth C],
BL [auth b],
CE [auth C],
CL [auth b],
CO [auth d],
DE [auth C],
DL [auth b],
DO [auth d],
EO [auth d],
JF [auth D],
KF [auth D],
KM [auth c],
LF [auth D],
LM [auth c],
MB [auth B],
MM [auth c],
NB [auth B],
NM [auth c],
OB [auth B],
OK [auth b],
OM [auth c],
PB [auth B],
PK [auth b],
PM [auth c],
QB [auth B],
QK [auth b],
QM [auth c],
RA [auth A],
RB [auth B],
RD [auth C],
RK [auth b],
RM [auth c],
SA [auth A],
SB [auth B],
SD [auth C],
SK [auth b],
SM [auth c],
TB [auth B],
TD [auth C],
TK [auth b],
TM [auth c],
UA [auth A],
UB [auth B],
UD [auth C],
UJ [auth a],
UK [auth b],
UM [auth c],
VB [auth B],
VD [auth C],
VJ [auth a],
VK [auth b],
VM [auth c],
WB [auth B],
WD [auth C],
WK [auth b],
WM [auth c],
XB [auth B],
XD [auth C],
XJ [auth a],
XK [auth b],
YB [auth B],
YD [auth C],
YK [auth b],
ZB [auth B],
ZD [auth C],
ZK [auth b]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
PHO
Query on PHO
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AO [auth d],
HF [auth D],
TA [auth A],
WJ [auth a]		PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
SQD
Query on SQD
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AK [auth a]
BB [auth A]
EK [auth a]
EQ [auth l]
HB [auth A]
AK [auth a],
BB [auth A],
EK [auth a],
EQ [auth l],
HB [auth A],
HP [auth h],
LK [auth a],
LR [auth x],
QG [auth F],
TL [auth b],
XA [auth A]
1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
C41 H78 O12 S
RVUUQPKXGDTQPG-JUDHQOGESA-N
LMG
Query on LMG
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BK [auth a]
CN [auth c]
DN [auth c]
FC [auth B]
HL [auth b]
BK [auth a],
CN [auth c],
DN [auth c],
FC [auth B],
HL [auth b],
JE [auth C],
KE [auth C],
KH [auth J],
LO [auth d],
PR [auth z],
QE [auth C],
SC [auth B],
VP [auth j],
YA [auth A]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
PL9
Query on PL9
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GO [auth d],
NF [auth D],
WA [auth A],
ZJ [auth a]		2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE
C53 H80 O2
FKUYMLZIRPABFK-UHFFFAOYSA-N
LHG
Query on LHG
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AG [auth E]
DB [auth A]
DQ [auth l]
GK [auth a]
IO [auth d]
AG [auth E],
DB [auth A],
DQ [auth l],
GK [auth a],
IO [auth d],
JO [auth d],
KO [auth d],
PF [auth D],
QC [auth B],
QF [auth D],
RF [auth D],
RO [auth e]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
HEC
Query on HEC
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ER [auth v],
SI [auth V]		HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
HEM
Query on HEM
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MG [auth E],
XO [auth e]		PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
BCR
Query on BCR
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CC [auth B]
CQ [auth k]
DC [auth B]
EC [auth B]
EE [auth C]
CC [auth B],
CQ [auth k],
DC [auth B],
EC [auth B],
EE [auth C],
EL [auth b],
FE [auth C],
FL [auth b],
FO [auth d],
FP [auth h],
GL [auth b],
KI [auth T],
KN [auth c],
MF [auth D],
PE [auth C],
SG [auth H],
TH [auth K],
VA [auth A],
WQ [auth t],
XM [auth c],
YJ [auth a],
YM [auth c]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMT
Query on LMT
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CB [auth A]
CR [auth u]
DH [auth I]
EN [auth c]
GC [auth B]
CB [auth A],
CR [auth u],
DH [auth I],
EN [auth c],
GC [auth B],
GQ [auth m],
HQ [auth m],
IJ [auth Y],
IL [auth b],
MH [auth J],
OG [auth F],
OJ [auth a],
WH [auth M],
XE [auth C],
XH [auth M],
XP [auth j],
XQ [auth t],
YO [auth f]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
2PE
Query on 2PE
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FJ [auth V]NONAETHYLENE GLYCOL
C18 H38 O10
YZUUTMGDONTGTN-UHFFFAOYSA-N
PE8
Query on PE8
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TP [auth i]3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL
C16 H34 O9
GLZWNFNQMJAZGY-UHFFFAOYSA-N
OEX
Query on OEX
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MA [auth A],
PJ [auth a]		CA-MN4-O5 CLUSTER
Ca Mn4 O5
SEXWDHMBWJEXOJ-UHFFFAOYSA-N
HTG
Query on HTG
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AI [auth O]
DP [auth h]
FK [auth a]
FN [auth c]
GN [auth c]
AI [auth O],
DP [auth h],
FK [auth a],
FN [auth c],
GN [auth c],
HC [auth B],
IC [auth B],
JL [auth b],
KL [auth b],
KQ [auth o],
LE [auth C],
ME [auth C],
NN [auth c],
OC [auth B],
ON [auth c],
PC [auth B],
RG [auth H],
RL [auth b],
SL [auth b],
TE [auth C],
TI [auth V],
UE [auth C],
VE [auth C],
WE [auth C]
heptyl 1-thio-beta-D-glucopyranoside
C13 H26 O5 S
HPEGNLMTTNTJSP-LBELIVKGSA-N
P6G
Query on P6G
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AQ [auth j]
FF [auth C]
IB [auth A]
IH [auth I]
IM [auth b]
AQ [auth j],
FF [auth C],
IB [auth A],
IH [auth I],
IM [auth b],
JB [auth A],
JD [auth B],
JG [auth E],
JM [auth b],
KD [auth B],
NI [auth T],
OO [auth d],
PO [auth d],
WF [auth D],
XF [auth D],
YF [auth D],
YN [auth c]
HEXAETHYLENE GLYCOL
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N
1PE
Query on 1PE
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BQ [auth j]
GJ [auth V]
LD [auth B]
MD [auth B]
OR [auth x]
BQ [auth j],
GJ [auth V],
LD [auth B],
MD [auth B],
OR [auth x],
VH [auth L],
VO [auth e]
PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
PG4
Query on PG4
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AD [auth B]
AF [auth C]
AJ [auth V]
BD [auth B]
BF [auth C]
AD [auth B],
AF [auth C],
AJ [auth V],
BD [auth B],
BF [auth C],
BG [auth E],
BJ [auth V],
CF [auth C],
CG [auth E],
CJ [auth V],
EB [auth A],
EH [auth I],
FH [auth I],
FQ [auth l],
GH [auth I],
HK [auth a],
IK [auth a],
IP [auth h],
KJ [auth X],
LJ [auth X],
MJ [auth X],
MR [auth x],
NH [auth J],
NO [auth d],
NP [auth i],
OH [auth J],
OP [auth i],
PI [auth U],
PN [auth c],
PP [auth i],
QN [auth c],
QP [auth i],
RN [auth c],
SN [auth c],
TO [auth e],
UC [auth B],
UF [auth D],
UG [auth H],
UH [auth K],
UL [auth b],
UO [auth e],
VC [auth B],
VG [auth H],
VL [auth b],
WC [auth B],
WG [auth H],
WL [auth b],
XC [auth B],
XG [auth H],
XL [auth b],
YC [auth B],
YE [auth C],
YI [auth V],
YP [auth j],
ZC [auth B],
ZE [auth C],
ZI [auth V]
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
PGE
Query on PGE
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AH [auth H]
AM [auth b]
BH [auth H]
BM [auth b]
CD [auth B]
AH [auth H],
AM [auth b],
BH [auth H],
BM [auth b],
CD [auth B],
CM [auth b],
CP [auth f],
DD [auth B],
DF [auth C],
DG [auth E],
DJ [auth V],
DM [auth b],
ED [auth B],
EF [auth C],
EG [auth E],
EJ [auth V],
EM [auth b],
FB [auth A],
FD [auth B],
FG [auth E],
FI [auth O],
FM [auth b],
GB [auth A],
GD [auth B],
GG [auth E],
GI [auth O],
GM [auth b],
HD [auth B],
HG [auth E],
HH [auth I],
HI [auth O],
HM [auth b],
ID [auth B],
IG [auth E],
JJ [auth Y],
JK [auth a],
JP [auth h],
KK [auth a],
KP [auth h],
LP [auth h],
MI [auth T],
MP [auth h],
NR [auth x],
PH [auth J],
PQ [auth o],
QH [auth J],
QQ [auth o],
RH [auth J],
RP [auth i],
RQ [auth o],
SP [auth i],
SQ [auth o],
TN [auth c],
UN [auth c],
VF [auth D],
VN [auth c],
WN [auth c],
XN [auth c],
YG [auth H],
YL [auth b],
YQ [auth t],
ZG [auth H],
ZL [auth b],
ZP [auth j],
ZQ [auth t]
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
GOL
Query on GOL
Download Ideal Coordinates CCD File 
AB [auth A]
AP [auth f]
AR [auth u]
BI [auth O]
BO [auth d]
AB [auth A],
AP [auth f],
AR [auth u],
BI [auth O],
BO [auth d],
BP [auth f],
BR [auth u],
CI [auth O],
CK [auth a],
DI [auth O],
DK [auth a],
EI [auth O],
FR [auth v],
GR [auth v],
HR [auth v],
IF [auth D],
IN [auth c],
IQ [auth m],
IR [auth v],
JC [auth B],
JI [auth T],
JN [auth c],
JR [auth v],
KC [auth B],
KR [auth y],
LC [auth B],
LI [auth T],
LL [auth b],
LN [auth c],
MC [auth B],
ML [auth b],
MN [auth c],
MO [auth d],
MQ [auth o],
NC [auth B],
NE [auth C],
NG [auth F],
NL [auth b],
NQ [auth o],
OE [auth C],
OI [auth U],
OL [auth b],
OQ [auth o],
PL [auth b],
QI [auth V],
QL [auth b],
RC [auth B],
RE [auth C],
SE [auth C],
SF [auth D],
SO [auth e],
TC [auth B],
TF [auth D],
UI [auth V],
VI [auth V],
VQ [auth t],
WI [auth V],
XI [auth V],
ZA [auth A],
ZH [auth O]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO
Query on EDO
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CH [auth H]
GF [auth C]
HJ [auth V]
II [auth O]
JH [auth I]
CH [auth H],
GF [auth C],
HJ [auth V],
II [auth O],
JH [auth I],
KB [auth A],
KG [auth E],
LG [auth E],
MK [auth a],
ND [auth B],
NJ [auth X],
OD [auth B],
PD [auth B],
QD [auth B],
QO [auth d],
SH [auth J],
TQ [auth o],
UP [auth i],
UQ [auth o],
WO [auth e],
ZF [auth D],
ZN [auth c]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
BCT
Query on BCT
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JQ [auth m],
QA [auth A],
TJ [auth a]		BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
FE2
Query on FE2
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NA [auth A],
QJ [auth a]		FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
CA
Query on CA
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EP [auth h]
HN [auth c]
LB [auth B]
LQ [auth o]
NK [auth b]
EP [auth h],
HN [auth c],
LB [auth B],
LQ [auth o],
NK [auth b],
YH [auth O]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL
Query on CL
Download Ideal Coordinates CCD File 
DR [auth v]
OA [auth A]
PA [auth A]
RI [auth V]
RJ [auth a]
DR [auth v],
OA [auth A],
PA [auth A],
RI [auth V],
RJ [auth a],
SJ [auth a]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG
Download Ideal Coordinates CCD File 
LH [auth J],
PG [auth F],
WP [auth j],
ZO [auth f]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
MHS
Query on MHS		D,
W [auth d]		L-PEPTIDE LINKINGC7 H11 N3 O2HIS
FME
Query on FME		AA [auth i],
H [auth I]		L-PEPTIDE LINKINGC6 H11 N O3 SMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.163 (Depositor), 0.160 (DCC) 
  • R-Value Work:  0.092 (Depositor), 0.090 (DCC) 
  • R-Value Observed: 0.095 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 122.19α = 90
b = 228.51β = 90
c = 286.4γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-08-30
    Type: Initial release
  • Version 1.1: 2017-10-25
    Changes: Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Derived calculations, Structure summary
  • Version 2.0: 2021-03-10
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 3.0: 2023-10-04
    Changes: Data collection, Database references, Non-polymer description, Refinement description