5HAL | pdb_00005hal

Crystal Structure of a putative beta-lactamase from Burkholderia vietnamiensis

PDB DOI: https://doi.org/10.2210/pdb5HAL/pdb

Classification: HYDROLASE
Organism(s): Burkholderia vietnamiensis G4
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2015-12-30 Released: 2016-01-13
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free:
0.187 (Depositor), 0.186 (DCC)
R-Value Work:
0.163 (Depositor), 0.163 (DCC)
R-Value Observed:
0.164 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 5HAL

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

Literature

Crystal Structure of a putative beta-lactamase from Burkholderia vietnamiensis

Seattle Structural Genomics Center for Infectious Disease (SSGCID), Dranow, D.M., Davies, D.R., Lorimer, D., Edwards, T.E.

To be published.

Macromolecule Content

Total Structure Weight: 12.93 kDa
Atom Count: 902
Modeled Residue Count: 103
Deposited Residue Count: 115
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	A	115	Burkholderia vietnamiensis G4	Mutation(s): 0 Gene Names: Bcep1808_3604
UniProt
Find proteins for A4JJY8 (Burkholderia vietnamiensis (strain G4 / LMG 22486)) Explore A4JJY8 Go to UniProtKB: A4JJY8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A4JJY8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.187 (Depositor), 0.186 (DCC)
R-Value Work: 0.163 (Depositor), 0.163 (DCC)
R-Value Observed: 0.164 (Depositor)

Diffraction Data:

Space Group: I 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.84	α = 90
b = 110.84	β = 90
c = 110.84	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2016-01-13

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2016-01-13
Type: Initial release
Version 1.1: 2016-02-03
Changes: Database references
Version 1.2: 2017-11-01
Changes: Author supporting evidence, Derived calculations
Version 1.3: 2024-03-06
Changes: Data collection, Database references
Version 1.4: 2025-10-22
Changes: Database references, Structure summary

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.