3RPL | pdb_00003rpl

D-fructose 1,6-bisphosphatase class 2/sedoheptulose 1,7-bisphosphatase of Synechocystis sp. PCC 6803 in complex with FRUCTOSE-1,6-BISPHOSPHATE

PDB DOI: https://doi.org/10.2210/pdb3RPL/pdb

Classification: HYDROLASE
Organism(s): Synechocystis sp. PCC 6803
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2011-04-26 Released: 2012-05-02
Deposition Author(s): Hu, X., Hui, D., Lingling, F., Jian, W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.207 (Depositor), 0.200 (DCC)
R-Value Work:
0.166 (Depositor), 0.160 (DCC)
R-Value Observed:
0.168 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

New insights into the structural and interactional basis for a promising route towards fructose-1,6-/sedoheptulose-1,7-bisphosphatases controlling

Hu, X., Lingling, F.

To be published.

Macromolecule Content

Total Structure Weight: 166.98 kDa
Atom Count: 11,262
Modeled Residue Count: 1,389
Deposited Residue Count: 1,516
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-fructose 1,6-bisphosphatase class 2/sedoheptulose 1,7-bisphosphatase	A, C, D	379	Synechocystis sp. PCC 6803	Mutation(s): 0 Gene Names: slr2094 EC: 3.1.3.11 (PDB Primary Data), 3.1.3.37 (PDB Primary Data)
UniProt
Find proteins for P73922 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa)) Explore P73922 Go to UniProtKB: P73922
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P73922
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
D-fructose 1,6-bisphosphatase class 2/sedoheptulose 1,7-bisphosphatase	B	379	Synechocystis sp. PCC 6803	Mutation(s): 0 Gene Names: slr2094 EC: 3.1.3.11 (PDB Primary Data), 3.1.3.37 (PDB Primary Data)
UniProt
Find proteins for P73922 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa)) Explore P73922 Go to UniProtKB: P73922
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P73922
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AMP Query on AMP Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain IA [auth D] SDF format, chain N [auth B] SDF format, chain Z [auth C] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth D] MOL2 format, chain N [auth B] MOL2 format, chain Z [auth C] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth D] mmCIF format, chain N [auth B] mmCIF format, chain Z [auth C]	I [auth A], IA [auth D], N [auth B], Z [auth C]	ADENOSINE MONOPHOSPHATE C₁₀ H₁₄ N₅ O₇ P UDMBCSSLTHHNCD-KQYNXXCUSA-N		Interactions Focus chain I [auth A] Focus chain IA [auth D] Focus chain N [auth B] Focus chain Z [auth C] Interactions & Density Focus chain I [auth A] Focus chain IA [auth D] Focus chain N [auth B] Focus chain Z [auth C]
FBP Query on FBP Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain R [auth B] SDF format, chain Y [auth C] SDF format, chain MA [auth D] MOL2 format, chain H [auth A] MOL2 format, chain R [auth B] MOL2 format, chain Y [auth C] MOL2 format, chain MA [auth D] mmCIF format, chain H [auth A] mmCIF format, chain R [auth B] mmCIF format, chain Y [auth C] mmCIF format, chain MA [auth D]	H [auth A], MA [auth D], R [auth B], Y [auth C]	1,6-di-O-phosphono-beta-D-fructofuranose C₆ H₁₄ O₁₂ P₂ RNBGYGVWRKECFJ-ARQDHWQXSA-N		Interactions Focus chain H [auth A] Focus chain MA [auth D] Focus chain R [auth B] Focus chain Y [auth C] Interactions & Density Focus chain H [auth A] Focus chain MA [auth D] Focus chain R [auth B] Focus chain Y [auth C]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain BA [auth C] SDF format, chain CA [auth C] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain NA [auth D] SDF format, chain OA [auth D] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain U [auth B] MOL2 format, chain AA [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain NA [auth D] MOL2 format, chain OA [auth D] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] mmCIF format, chain AA [auth C] mmCIF format, chain BA [auth C] mmCIF format, chain CA [auth C] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain NA [auth D] mmCIF format, chain OA [auth D] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B]	AA [auth C] BA [auth C] CA [auth C] J [auth A] K [auth A] AA [auth C], BA [auth C], CA [auth C], J [auth A], K [auth A], L [auth A], NA [auth D], OA [auth D], S [auth B], T [auth B], U [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain NA [auth D] Focus chain OA [auth D] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain NA [auth D] Focus chain OA [auth D] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain HA [auth C] MOL2 format, chain HA [auth C] mmCIF format, chain HA [auth C]	HA [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain HA [auth C] Interactions & Density Focus chain HA [auth C]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain DA [auth C] SDF format, chain EA [auth C] SDF format, chain GA [auth C] SDF format, chain M [auth A] SDF format, chain PA [auth D] SDF format, chain FA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain EA [auth C] MOL2 format, chain GA [auth C] MOL2 format, chain M [auth A] MOL2 format, chain PA [auth D] MOL2 format, chain FA [auth C] mmCIF format, chain DA [auth C] mmCIF format, chain EA [auth C] mmCIF format, chain GA [auth C] mmCIF format, chain M [auth A] mmCIF format, chain PA [auth D] mmCIF format, chain FA [auth C]	DA [auth C] EA [auth C] FA [auth C] GA [auth C] M [auth A] DA [auth C], EA [auth C], FA [auth C], GA [auth C], M [auth A], PA [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain M [auth A] Focus chain PA [auth D] Interactions & Density Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain M [auth A] Focus chain PA [auth D]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain JA [auth D] SDF format, chain KA [auth D] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain V [auth C] SDF format, chain W [auth C] SDF format, chain X [auth C] SDF format, chain LA [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain JA [auth D] MOL2 format, chain KA [auth D] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C] MOL2 format, chain LA [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain JA [auth D] mmCIF format, chain KA [auth D] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain V [auth C] mmCIF format, chain W [auth C] mmCIF format, chain X [auth C] mmCIF format, chain LA [auth D]	E [auth A] F [auth A] G [auth A] JA [auth D] KA [auth D] E [auth A], F [auth A], G [auth A], JA [auth D], KA [auth D], LA [auth D], O [auth B], P [auth B], Q [auth B], V [auth C], W [auth C], X [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain JA [auth D] Focus chain KA [auth D] Focus chain LA [auth D] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain JA [auth D] Focus chain KA [auth D] Focus chain LA [auth D] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO Query on CSO	B	L-PEPTIDE LINKING	C₃ H₇ N O₃ S		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.207 (Depositor), 0.200 (DCC)
R-Value Work: 0.166 (Depositor), 0.160 (DCC)
R-Value Observed: 0.168 (Depositor)

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 145.222	α = 90
b = 145.222	β = 90
c = 169.104	γ = 120

Software Package:

Software Name	Purpose
CrysalisPro	data collection
MOLREP	phasing
PHENIX	refinement
CrysalisPro	data reduction
SCALA	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-05-02

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-05-02
Type: Initial release
Version 1.1: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Database references, Derived calculations, Structure summary
Version 1.2: 2023-11-01
Changes: Data collection, Database references, Refinement description, Structure summary
Version 1.3: 2023-12-06
Changes: Data collection
Version 1.4: 2024-10-30
Changes: Structure summary