3HJB | pdb_00003hjb

1.5 Angstrom Crystal Structure of Glucose-6-phosphate Isomerase from Vibrio cholerae.

• PDB DOI: https://doi.org/10.2210/pdb3HJB/pdb

• Classification: ISOMERASE
• Organism(s): Vibrio cholerae
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2009-05-21 Released: 2009-06-16 
• Deposition Author(s): Minasov, G., Halavaty, A., Shuvalova, L., Dubrovska, I., Winsor, J., Papazisi, L., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.151 (Depositor), 0.162 (DCC) 
• R-Value Work: 
  0.127 (Depositor), 0.140 (DCC) 
• R-Value Observed: 
  0.128 (Depositor) 

Starting Model: experimental

Literature

1.5 Angstrom Crystal Structure of Glucose-6-phosphate Isomerase from Vibrio cholerae.

Minasov, G., Halavaty, A., Shuvalova, L., Dubrovska, I., Winsor, J., Papazisi, L., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 255.75 kDa 
• Atom Count: 22,629 
• Modeled Residue Count: 2,204 
• Deposited Residue Count: 2,296 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucose-6-phosphate isomerase	A, B, C, D	574	Vibrio cholerae	Mutation(s): 1  Gene Names: pgi, VC_0374 EC: 5.3.1.9
UniProt
Find proteins for Q9KUY4 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KUY4  Go to UniProtKB:  Q9KUY4

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PG4	P [auth A], VA [auth D]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
PEG	AA [auth B], IA [auth C], JA [auth C], KA [auth C]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
CA	BA [auth C], E [auth A], F [auth A], G [auth A], H [auth A], LA [auth D], MA [auth D], NA [auth D], Q [auth B], R [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	CA [auth C], DA [auth C], EA [auth C], FA [auth C], GA [auth C], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], OA [auth D], PA [auth D], QA [auth D], RA [auth D], S [auth B], SA [auth D], T [auth B], TA [auth D], U [auth B], UA [auth D], V [auth B], W [auth B], X [auth B], Y [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	HA [auth C], Z [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.151 (Depositor), 0.162 (DCC) 
• R-Value Work:  0.127 (Depositor), 0.140 (DCC) 
• R-Value Observed: 0.128 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m33hjb

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 125.661	α = 90
b = 75.094	β = 90.21
c = 127.456	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-06-16 
Deposition Author(s): Minasov, G., Halavaty, A., Shuvalova, L., Dubrovska, I., Winsor, J., Papazisi, L., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2009-06-16
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Advisory, Refinement description
• Version 1.3: 2021-10-13
  Changes: Advisory, Database references, Derived calculations
• Version 1.4: 2023-09-06
  Changes: Data collection, Refinement description