4QKU | pdb_00004qku

Crystal structure of a putative hydrolase from Burkholderia cenocepacia

PDB DOI: https://doi.org/10.2210/pdb4QKU/pdb

Classification: HYDROLASE
Organism(s): Burkholderia cenocepacia J2315
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2014-06-09 Released: 2014-06-25
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free:
0.249 (Depositor), 0.253 (DCC)
R-Value Work:
0.208 (Depositor), 0.213 (DCC)
R-Value Observed:
0.210 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of a putative hydrolase from Burkholderia cenocepacia

Edwards, T.E., Fairman, J.W., Seattle Structural Genomics Center for Infectious Disease (SSGCID)

To be published.

Macromolecule Content

Total Structure Weight: 192.34 kDa
Atom Count: 13,340
Modeled Residue Count: 1,695
Deposited Residue Count: 1,764
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
hydrolase	A, B, C, D	441	Burkholderia cenocepacia J2315	Mutation(s): 0 Gene Names: BCAL3183 EC: 3.7.1.2
UniProt
Find proteins for B4ECX4 (Burkholderia cenocepacia (strain ATCC BAA-245 / DSM 16553 / LMG 16656 / NCTC 13227 / J2315 / CF5610)) Explore B4ECX4 Go to UniProtKB: B4ECX4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B4ECX4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain Q [auth D] SDF format, chain N [auth C] SDF format, chain M [auth C] SDF format, chain J [auth B] SDF format, chain G [auth A] MOL2 format, chain Q [auth D] MOL2 format, chain N [auth C] MOL2 format, chain M [auth C] MOL2 format, chain J [auth B] MOL2 format, chain G [auth A] mmCIF format, chain Q [auth D] mmCIF format, chain N [auth C] mmCIF format, chain M [auth C] mmCIF format, chain J [auth B] mmCIF format, chain G [auth A]	G [auth A], J [auth B], M [auth C], N [auth C], Q [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain Q [auth D] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain Q [auth D]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain P [auth D] SDF format, chain L [auth C] SDF format, chain I [auth B] SDF format, chain F [auth A] MOL2 format, chain P [auth D] MOL2 format, chain L [auth C] MOL2 format, chain I [auth B] MOL2 format, chain F [auth A] mmCIF format, chain P [auth D] mmCIF format, chain L [auth C] mmCIF format, chain I [auth B] mmCIF format, chain F [auth A]	F [auth A], I [auth B], L [auth C], P [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain P [auth D] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain P [auth D]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain O [auth D] SDF format, chain K [auth C] SDF format, chain H [auth B] SDF format, chain E [auth A] MOL2 format, chain O [auth D] MOL2 format, chain K [auth C] MOL2 format, chain H [auth B] MOL2 format, chain E [auth A] mmCIF format, chain O [auth D] mmCIF format, chain K [auth C] mmCIF format, chain H [auth B] mmCIF format, chain E [auth A]	E [auth A], H [auth B], K [auth C], O [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain O [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain O [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free: 0.249 (Depositor), 0.253 (DCC)
R-Value Work: 0.208 (Depositor), 0.213 (DCC)
R-Value Observed: 0.210 (Depositor)

Diffraction Data:

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.64	α = 90
b = 110.55	β = 106.61
c = 116.16	γ = 90

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

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2014-06-25

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2014-06-25
Type: Initial release
Version 1.1: 2024-02-28
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2025-10-22
Changes: Database references, Structure summary