4BGU | pdb_00004bgu

1.50 A resolution structure of the malate dehydrogenase from Haloferax volcanii

• PDB DOI: https://doi.org/10.2210/pdb4BGU/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Haloferax volcanii
• Mutation(s): No 


• Deposited: 2013-03-28 Released: 2014-04-16 
• Deposition Author(s): Talon, R., Madern, D., Girard, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.49 Å
• R-Value Free: 
  0.179 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.156 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.157 (Depositor) 

Literature

Insight Into Structural Evolution of Extremophilic Proteins

Talon, R., Girard, E., Franzetti, B., Zaccai, G., Madern, D.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 135.51 kDa 
• Atom Count: 11,435 
• Modeled Residue Count: 1,212 
• Deposited Residue Count: 1,212 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MALATE DEHYDROGENASE	A, B, C, D	303	Haloferax volcanii	Mutation(s): 0  EC: 1.1.1.37
UniProt
Find proteins for Q9P9L2 (Haloferax volcanii (strain ATCC 29605 / DSM 3757 / JCM 8879 / NBRC 14742 / NCIMB 2012 / VKM B-1768 / DS2)) Explore Q9P9L2  Go to UniProtKB:  Q9P9L2

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
P33	HA [auth A]	3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL C14 H30 O8 XPJRQAIZZQMSCM-UHFFFAOYSA-N
1PE	FB [auth B], GA [auth A]	PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N
PG4	CC [auth C], DC [auth C]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
PGE	DD [auth D], EB [auth B], FA [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
TRS	DB [auth B], EA [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
K	E [auth A], EC [auth D], F [auth A], FC [auth D], G [auth A], GB [auth C], GC [auth D], H [auth A], HB [auth C], HC [auth D], I [auth A], IA [auth B], IB [auth C], IC [auth D], J [auth A], JA [auth B], JB [auth C], K [auth A], KA [auth B], KB [auth C], LA [auth B], LB [auth C], MB [auth C]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL	AA [auth A], AB [auth B], AC [auth C], AD [auth D], BA [auth A], BB [auth B], BC [auth C], BD [auth D], CA [auth A], CB [auth B], CD [auth D], DA [auth A], JC [auth D], KC [auth D], L [auth A], LC [auth D], M [auth A], MA [auth B], MC [auth D], N [auth A], NA [auth B], NB [auth C], NC [auth D], O [auth A], OA [auth B], OB [auth C], OC [auth D], P [auth A], PA [auth B], PB [auth C], PC [auth D], Q [auth A], QA [auth B], QB [auth C], QC [auth D], R [auth A], RA [auth B], RB [auth C], RC [auth D], S [auth A], SA [auth B], SB [auth C], SC [auth D], T [auth A], TA [auth B], TB [auth C], TC [auth D], U [auth A], UA [auth B], UB [auth C], UC [auth D], V [auth A], VA [auth B], VB [auth C], VC [auth D], W [auth A], WA [auth B], WB [auth C], WC [auth D], X [auth A], XA [auth B], XB [auth C], XC [auth D], Y [auth A], YA [auth B], YB [auth C], YC [auth D], Z [auth A], ZA [auth B], ZB [auth C], ZC [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.49 Å
• R-Value Free:  0.179 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.156 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.157 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 143.76	α = 90
b = 82.319	β = 101.72
c = 112.75	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-04-16 
Deposition Author(s): Talon, R., Madern, D., Girard, E.

Revision History  

• Version 1.0: 2014-04-16
  Type: Initial release
  
• Version 1.1: 2019-03-06
  Changes: Data collection, Experimental preparation, Other
• Version 1.2: 2024-05-08
  Changes: Data collection, Database references, Derived calculations, Other, Structure summary