4LHR | pdb_00004lhr

Crystal structure of a deoxyuridine 5'-triphosphate nucleotidohydrolase from Burkholderia thailandensis

PDB DOI: https://doi.org/10.2210/pdb4LHR/pdb

Classification: HYDROLASE
Organism(s): Burkholderia thailandensis E264
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2013-07-01 Released: 2013-08-07
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.135 (Depositor), 0.151 (DCC)
R-Value Work:
0.117 (Depositor), 0.141 (DCC)
R-Value Observed:
0.118 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 4LHR

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

Literature

Crystal structure of a deoxyuridine 5'-triphosphate nucleotidohydrolase from Burkholderia thailandensis

Edwards, T.E., Abendroth, J., Seattle Structural Genomics Center for Infectious Disease

To be published.

Macromolecule Content

Total Structure Weight: 17.03 kDa
Atom Count: 1,256
Modeled Residue Count: 134
Deposited Residue Count: 156
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Deoxyuridine 5'-triphosphate nucleotidohydrolase	A	156	Burkholderia thailandensis E264	Mutation(s): 0 Gene Names: BTH_I0767, dut EC: 3.6.1.23
UniProt
Find proteins for Q2T0H6 (Burkholderia thailandensis (strain ATCC 700388 / DSM 13276 / CCUG 48851 / CIP 106301 / E264)) Explore Q2T0H6 Go to UniProtKB: Q2T0H6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q2T0H6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PG4 Query on PG4 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]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-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: 1.50 Å
R-Value Free: 0.135 (Depositor), 0.151 (DCC)
R-Value Work: 0.117 (Depositor), 0.141 (DCC)
R-Value Observed: 0.118 (Depositor)

Diffraction Data:

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.36	α = 90
b = 84.36	β = 90
c = 54.62	γ = 120

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: 2013-08-07

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2013-08-07
Type: Initial release
Version 1.1: 2017-10-11
Changes: Data collection
Version 1.2: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description

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.