4EM6 | pdb_00004em6

The structure of Glucose-6-phosphate isomerase (GPI) from Brucella melitensis

PDB DOI: https://doi.org/10.2210/pdb4EM6/pdb

Classification: ISOMERASE
Organism(s): Brucella melitensis bv. 1 str. 16M
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-04-11 Released: 2012-05-02
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.169 (Depositor), 0.180 (DCC)
R-Value Work:
0.131 (Depositor), 0.140 (DCC)
R-Value Observed:
0.133 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

The structure of Glucose-6-phosphate isomerase (GPI) from Brucella melitensis

Clifton, M.C., Edwards, T.E., Seattle Structural Genomics Center for Infectious Disease (SSGCID)

To be published.

Macromolecule Content

Total Structure Weight: 240.78 kDa
Atom Count: 19,246
Modeled Residue Count: 2,182
Deposited Residue Count: 2,212
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 [auth D], B [auth A], C [auth B], D [auth C]	553	Brucella melitensis bv. 1 str. 16M	Mutation(s): 0 Gene Names: pgi, BMEI1636 EC: 5.3.1.9
UniProt
Find proteins for Q8YF86 (Brucella melitensis biotype 1 (strain ATCC 23456 / CCUG 17765 / NCTC 10094 / 16M)) Explore Q8YF86 Go to UniProtKB: Q8YF86
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8YF86
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain N [auth C] MOL2 format, chain N [auth C] mmCIF format, chain N [auth C]	N [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain N [auth C] Interactions & Density Focus chain N [auth C]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain F [auth D] SDF format, chain G [auth A] SDF format, chain K [auth B] SDF format, chain M [auth B] SDF format, chain P [auth C] SDF format, chain Q [auth C] SDF format, chain R [auth C] SDF format, chain U [auth C] MOL2 format, chain F [auth D] MOL2 format, chain G [auth A] MOL2 format, chain K [auth B] MOL2 format, chain M [auth B] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C] MOL2 format, chain U [auth C] mmCIF format, chain F [auth D] mmCIF format, chain G [auth A] mmCIF format, chain K [auth B] mmCIF format, chain M [auth B] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain R [auth C] mmCIF format, chain U [auth C]	F [auth D] G [auth A] K [auth B] M [auth B] P [auth C] F [auth D], G [auth A], K [auth B], M [auth B], P [auth C], Q [auth C], R [auth C], U [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain F [auth D] Focus chain G [auth A] Focus chain K [auth B] Focus chain M [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Focus chain U [auth C] Interactions & Density Focus chain F [auth D] Focus chain G [auth A] Focus chain K [auth B] Focus chain M [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Focus chain U [auth C]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain E [auth D] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth B] SDF format, chain L [auth B] SDF format, chain O [auth C] SDF format, chain S [auth C] SDF format, chain T [auth C] SDF format, chain V [auth C] MOL2 format, chain E [auth D] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth B] MOL2 format, chain L [auth B] MOL2 format, chain O [auth C] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] MOL2 format, chain V [auth C] mmCIF format, chain E [auth D] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth B] mmCIF format, chain L [auth B] mmCIF format, chain O [auth C] mmCIF format, chain S [auth C] mmCIF format, chain T [auth C] mmCIF format, chain V [auth C]	E [auth D] H [auth A] I [auth A] J [auth B] L [auth B] E [auth D], H [auth A], I [auth A], J [auth B], L [auth B], O [auth C], S [auth C], T [auth C], V [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain E [auth D] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth B] Focus chain L [auth B] Focus chain O [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain V [auth C] Interactions & Density Focus chain E [auth D] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth B] Focus chain L [auth B] Focus chain O [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain V [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.169 (Depositor), 0.180 (DCC)
R-Value Work: 0.131 (Depositor), 0.140 (DCC)
R-Value Observed: 0.133 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.59	α = 95.42
b = 72.73	β = 91.54
c = 115.25	γ = 110.06

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2012-05-02

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2012-05-02
Type: Initial release
Version 1.1: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description