3HJB

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.151 (Depositor), 0.160 (DCC)
R-Value Work:
0.127 (Depositor), 0.140 (DCC)
R-Value Observed:
0.128 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

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.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9KUY4
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain P [auth A] SDF format, chain VA [auth D] MOL2 format, chain P [auth A] MOL2 format, chain VA [auth D] mmCIF format, chain P [auth A] mmCIF format, chain VA [auth D]	P [auth A], VA [auth D]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain P [auth A] Focus chain VA [auth D] Interactions & Density Focus chain P [auth A] Focus chain VA [auth D]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain IA [auth C] SDF format, chain JA [auth C] SDF format, chain KA [auth C] MOL2 format, chain AA [auth B] MOL2 format, chain IA [auth C] MOL2 format, chain JA [auth C] MOL2 format, chain KA [auth C] mmCIF format, chain AA [auth B] mmCIF format, chain IA [auth C] mmCIF format, chain JA [auth C] mmCIF format, chain KA [auth C]	AA [auth B], IA [auth C], JA [auth C], KA [auth C]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain KA [auth C] Interactions & Density Focus chain AA [auth B] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain KA [auth C]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain LA [auth D] SDF format, chain MA [auth D] SDF format, chain NA [auth D] SDF format, chain Q [auth B] SDF format, chain R [auth B] MOL2 format, chain BA [auth C] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain LA [auth D] MOL2 format, chain MA [auth D] MOL2 format, chain NA [auth D] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] mmCIF format, chain BA [auth C] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain LA [auth D] mmCIF format, chain MA [auth D] mmCIF format, chain NA [auth D] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B]	BA [auth C] E [auth A] F [auth A] G [auth A] H [auth A] 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		Interactions Focus chain BA [auth C] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain LA [auth D] Focus chain MA [auth D] Focus chain NA [auth D] Focus chain Q [auth B] Focus chain R [auth B] Interactions & Density Focus chain BA [auth C] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain LA [auth D] Focus chain MA [auth D] Focus chain NA [auth D] Focus chain Q [auth B] Focus chain R [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain CA [auth C] SDF format, chain DA [auth C] SDF format, chain EA [auth C] SDF format, chain FA [auth C] SDF format, chain GA [auth C] 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 N [auth A] SDF format, chain O [auth A] SDF format, chain OA [auth D] SDF format, chain PA [auth D] SDF format, chain QA [auth D] SDF format, chain RA [auth D] SDF format, chain S [auth B] SDF format, chain SA [auth D] SDF format, chain T [auth B] SDF format, chain TA [auth D] SDF format, chain U [auth B] SDF format, chain UA [auth D] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain Y [auth B] MOL2 format, chain CA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain EA [auth C] MOL2 format, chain FA [auth C] MOL2 format, chain GA [auth C] 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 N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth D] MOL2 format, chain PA [auth D] MOL2 format, chain QA [auth D] MOL2 format, chain RA [auth D] MOL2 format, chain S [auth B] MOL2 format, chain SA [auth D] MOL2 format, chain T [auth B] MOL2 format, chain TA [auth D] MOL2 format, chain U [auth B] MOL2 format, chain UA [auth D] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] mmCIF format, chain CA [auth C] mmCIF format, chain DA [auth C] mmCIF format, chain EA [auth C] mmCIF format, chain FA [auth C] mmCIF format, chain GA [auth C] 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 N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain OA [auth D] mmCIF format, chain PA [auth D] mmCIF format, chain QA [auth D] mmCIF format, chain RA [auth D] mmCIF format, chain S [auth B] mmCIF format, chain SA [auth D] mmCIF format, chain T [auth B] mmCIF format, chain TA [auth D] mmCIF format, chain U [auth B] mmCIF format, chain UA [auth D] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B] mmCIF format, chain Y [auth B]	CA [auth C] DA [auth C] EA [auth C] FA [auth C] GA [auth C] 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		Interactions Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain GA [auth C] 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 N [auth A] Focus chain O [auth A] Focus chain OA [auth D] Focus chain PA [auth D] Focus chain QA [auth D] Focus chain RA [auth D] Focus chain S [auth B] Focus chain SA [auth D] Focus chain T [auth B] Focus chain TA [auth D] Focus chain U [auth B] Focus chain UA [auth D] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Interactions & Density Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain GA [auth C] 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 N [auth A] Focus chain O [auth A] Focus chain OA [auth D] Focus chain PA [auth D] Focus chain QA [auth D] Focus chain RA [auth D] Focus chain S [auth B] Focus chain SA [auth D] Focus chain T [auth B] Focus chain TA [auth D] Focus chain U [auth B] Focus chain UA [auth D] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain HA [auth C] SDF format, chain Z [auth B] MOL2 format, chain HA [auth C] MOL2 format, chain Z [auth B] mmCIF format, chain HA [auth C] mmCIF format, chain Z [auth B]	HA [auth C], Z [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain HA [auth C] Focus chain Z [auth B] Interactions & Density Focus chain HA [auth C] Focus chain Z [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.151 (Depositor), 0.160 (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

View Full Validation Report

Entry History

Deposition Data

Released Date: 2009-06-16

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

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