3ROJ | pdb_00003roj

D-fructose 1,6-bisphosphatase class 2/sedoheptulose 1,7-bisphosphatase of Synechocystis sp. PCC 6803

PDB DOI: https://doi.org/10.2210/pdb3ROJ/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: 2.30 Å
R-Value Free:
0.204 (Depositor), 0.200 (DCC)
R-Value Work:
0.183 (Depositor), 0.180 (DCC)
R-Value Observed:
0.184 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 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: 166.74 kDa
Atom Count: 11,404
Modeled Residue Count: 1,385
Deposited Residue Count: 1,516
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(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, B, 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

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AMP Query on AMP Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain KA [auth C] SDF format, chain LA [auth C] SDF format, chain Y [auth B] MOL2 format, chain G [auth A] MOL2 format, chain KA [auth C] MOL2 format, chain LA [auth C] MOL2 format, chain Y [auth B] mmCIF format, chain G [auth A] mmCIF format, chain KA [auth C] mmCIF format, chain LA [auth C] mmCIF format, chain Y [auth B]	G [auth A], KA [auth C], LA [auth C], Y [auth B]	ADENOSINE MONOPHOSPHATE C₁₀ H₁₄ N₅ O₇ P UDMBCSSLTHHNCD-KQYNXXCUSA-N		Interactions Focus chain G [auth A] Focus chain KA [auth C] Focus chain LA [auth C] Focus chain Y [auth B] Interactions & Density Focus chain G [auth A] Focus chain KA [auth C] Focus chain LA [auth C] Focus chain Y [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain AB [auth D] SDF format, chain BA [auth B] SDF format, chain BB [auth D] SDF format, chain CA [auth B] SDF format, chain CB [auth D] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain MA [auth C] SDF format, chain NA [auth C] SDF format, chain OA [auth C] SDF format, chain PA [auth C] SDF format, chain YA [auth D] SDF format, chain ZA [auth D] MOL2 format, chain AB [auth D] MOL2 format, chain BA [auth B] MOL2 format, chain BB [auth D] MOL2 format, chain CA [auth B] MOL2 format, chain CB [auth D] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth C] MOL2 format, chain NA [auth C] MOL2 format, chain OA [auth C] MOL2 format, chain PA [auth C] MOL2 format, chain YA [auth D] MOL2 format, chain ZA [auth D] mmCIF format, chain AB [auth D] mmCIF format, chain BA [auth B] mmCIF format, chain BB [auth D] mmCIF format, chain CA [auth B] mmCIF format, chain CB [auth D] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth C] mmCIF format, chain NA [auth C] mmCIF format, chain OA [auth C] mmCIF format, chain PA [auth C] mmCIF format, chain YA [auth D] mmCIF format, chain ZA [auth D]	AB [auth D] BA [auth B] BB [auth D] CA [auth B] CB [auth D] AB [auth D], BA [auth B], BB [auth D], CA [auth B], CB [auth D], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], MA [auth C], NA [auth C], OA [auth C], PA [auth C], YA [auth D], ZA [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AB [auth D] Focus chain BA [auth B] Focus chain BB [auth D] Focus chain CA [auth B] Focus chain CB [auth D] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain MA [auth C] Focus chain NA [auth C] Focus chain OA [auth C] Focus chain PA [auth C] Focus chain YA [auth D] Focus chain ZA [auth D] Interactions & Density Focus chain AB [auth D] Focus chain BA [auth B] Focus chain BB [auth D] Focus chain CA [auth B] Focus chain CB [auth D] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain MA [auth C] Focus chain NA [auth C] Focus chain OA [auth C] Focus chain PA [auth C] Focus chain YA [auth D] Focus chain ZA [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain X [auth A] MOL2 format, chain X [auth A] mmCIF format, chain X [auth A]	X [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain X [auth A] Interactions & Density Focus chain X [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain DA [auth B] SDF format, chain DB [auth D] SDF format, chain EA [auth B] SDF format, chain EB [auth D] SDF format, chain FA [auth B] SDF format, chain GA [auth B] SDF format, chain HA [auth B] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain QA [auth C] SDF format, chain R [auth A] SDF format, chain RA [auth C] SDF format, chain S [auth A] SDF format, chain SA [auth C] SDF format, chain T [auth A] SDF format, chain TA [auth C] SDF format, chain U [auth A] SDF format, chain UA [auth C] SDF format, chain V [auth A] SDF format, chain VA [auth C] SDF format, chain W [auth A] MOL2 format, chain DA [auth B] MOL2 format, chain DB [auth D] MOL2 format, chain EA [auth B] MOL2 format, chain EB [auth D] MOL2 format, chain FA [auth B] MOL2 format, chain GA [auth B] MOL2 format, chain HA [auth B] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth C] MOL2 format, chain R [auth A] MOL2 format, chain RA [auth C] MOL2 format, chain S [auth A] MOL2 format, chain SA [auth C] MOL2 format, chain T [auth A] MOL2 format, chain TA [auth C] MOL2 format, chain U [auth A] MOL2 format, chain UA [auth C] MOL2 format, chain V [auth A] MOL2 format, chain VA [auth C] MOL2 format, chain W [auth A] mmCIF format, chain DA [auth B] mmCIF format, chain DB [auth D] mmCIF format, chain EA [auth B] mmCIF format, chain EB [auth D] mmCIF format, chain FA [auth B] mmCIF format, chain GA [auth B] mmCIF format, chain HA [auth B] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain QA [auth C] mmCIF format, chain R [auth A] mmCIF format, chain RA [auth C] mmCIF format, chain S [auth A] mmCIF format, chain SA [auth C] mmCIF format, chain T [auth A] mmCIF format, chain TA [auth C] mmCIF format, chain U [auth A] mmCIF format, chain UA [auth C] mmCIF format, chain V [auth A] mmCIF format, chain VA [auth C] mmCIF format, chain W [auth A]	DA [auth B] DB [auth D] EA [auth B] EB [auth D] FA [auth B] DA [auth B], DB [auth D], EA [auth B], EB [auth D], FA [auth B], GA [auth B], HA [auth B], N [auth A], O [auth A], P [auth A], Q [auth A], QA [auth C], R [auth A], RA [auth C], S [auth A], SA [auth C], T [auth A], TA [auth C], U [auth A], UA [auth C], V [auth A], VA [auth C], W [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain DA [auth B] Focus chain DB [auth D] Focus chain EA [auth B] Focus chain EB [auth D] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain HA [auth B] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain QA [auth C] Focus chain R [auth A] Focus chain RA [auth C] Focus chain S [auth A] Focus chain SA [auth C] Focus chain T [auth A] Focus chain TA [auth C] Focus chain U [auth A] Focus chain UA [auth C] Focus chain V [auth A] Focus chain VA [auth C] Focus chain W [auth A] Interactions & Density Focus chain DA [auth B] Focus chain DB [auth D] Focus chain EA [auth B] Focus chain EB [auth D] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain HA [auth B] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain QA [auth C] Focus chain R [auth A] Focus chain RA [auth C] Focus chain S [auth A] Focus chain SA [auth C] Focus chain T [auth A] Focus chain TA [auth C] Focus chain U [auth A] Focus chain UA [auth C] Focus chain V [auth A] Focus chain VA [auth C] Focus chain W [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain IA [auth C] SDF format, chain JA [auth C] SDF format, chain WA [auth D] SDF format, chain XA [auth D] SDF format, chain Z [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain IA [auth C] MOL2 format, chain JA [auth C] MOL2 format, chain WA [auth D] MOL2 format, chain XA [auth D] MOL2 format, chain Z [auth B] mmCIF format, chain AA [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain IA [auth C] mmCIF format, chain JA [auth C] mmCIF format, chain WA [auth D] mmCIF format, chain XA [auth D] mmCIF format, chain Z [auth B]	AA [auth B] E [auth A] F [auth A] IA [auth C] JA [auth C] AA [auth B], E [auth A], F [auth A], IA [auth C], JA [auth C], WA [auth D], XA [auth D], Z [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain E [auth A] Focus chain F [auth A] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain WA [auth D] Focus chain XA [auth D] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain E [auth A] Focus chain F [auth A] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain WA [auth D] Focus chain XA [auth D] Focus chain Z [auth B]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.204 (Depositor), 0.200 (DCC)
R-Value Work: 0.183 (Depositor), 0.180 (DCC)
R-Value Observed: 0.184 (Depositor)

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 144.282	α = 90
b = 144.282	β = 90
c = 168.795	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: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2023-12-06
Changes: Data collection
Version 1.3: 2024-10-16
Changes: Structure summary