4EFZ | pdb_00004efz

Crystal Structure of a hypothetical metallo-beta-lactamase from Burkholderia pseudomallei

PDB DOI: https://doi.org/10.2210/pdb4EFZ/pdb

Classification: HYDROLASE
Organism(s): Burkholderia pseudomallei 1710b
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-03-30 Released: 2012-05-09
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.197 (Depositor), 0.192 (DCC)
R-Value Work:
0.171 (Depositor), 0.166 (DCC)
R-Value Observed:
0.172 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Crystal Structure of a hypothetical metallo-beta-lactamase from Burkholderia pseudomallei

Fairman, J.W., Craig, T.K., Staker, B.L., Stewart, L.

To be published.

Macromolecule Content

Total Structure Weight: 65.92 kDa
Atom Count: 4,996
Modeled Residue Count: 584
Deposited Residue Count: 596
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Metallo-beta-lactamase family protein	A, B	298	Burkholderia pseudomallei 1710b	Mutation(s): 0 Gene Names: BURPS1710b_2304 EC: 3
UniProt
Find proteins for Q3JRV4 (Burkholderia pseudomallei (strain 1710b)) Explore Q3JRV4 Go to UniProtKB: Q3JRV4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q3JRV4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain R [auth B] SDF format, chain S [auth B] MOL2 format, chain H [auth A] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] mmCIF format, chain H [auth A] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B]	H [auth A], R [auth B], S [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain H [auth A] Focus chain R [auth B] Focus chain S [auth B] Interactions & Density Focus chain H [auth A] Focus chain R [auth B] Focus chain S [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B]	E [auth A] F [auth A] L [auth B] M [auth B] N [auth B] E [auth A], F [auth A], L [auth B], M [auth B], N [auth B], O [auth B], P [auth B], Q [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain I [auth B] MOL2 format, chain C [auth A] MOL2 format, chain I [auth B] mmCIF format, chain C [auth A] mmCIF format, chain I [auth B]	C [auth A], I [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain I [auth B] Interactions & Density Focus chain C [auth A] Focus chain I [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] MOL2 format, chain D [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] mmCIF format, chain D [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B]	D [auth A], J [auth B], K [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain D [auth A] Focus chain J [auth B] Focus chain K [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.197 (Depositor), 0.192 (DCC)
R-Value Work: 0.171 (Depositor), 0.166 (DCC)
R-Value Observed: 0.172 (Depositor)

Diffraction Data: https://doi.org/10.18430/M34EFZ

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.32	α = 90
b = 83.5	β = 90
c = 96.44	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2012-05-09

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2012-05-09
Type: Initial release
Version 1.1: 2018-01-24
Changes: Structure summary
Version 1.2: 2024-02-28
Changes: Data collection, Database references, Derived calculations
Version 1.3: 2025-10-22
Changes: Structure summary