5VM1 | pdb_00005vm1

Crystal structure of a xyloylose kinase from Brucella ovis

PDB DOI: https://doi.org/10.2210/pdb5VM1/pdb

Classification: TRANSFERASE
Organism(s): Brucella ovis ATCC 25840
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2017-04-26 Released: 2017-05-10
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free:
0.230 (Depositor), 0.230 (DCC)
R-Value Work:
0.166 (Depositor), 0.170 (DCC)
R-Value Observed:
0.169 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of a xyloylose kinase from

Edwards, T.E., Abendroth, J., Lorimer, D.D., Letesson, J.J., Seattle Structural Genomics Center for Infectious Disease (SSGCID)

To be published.

Macromolecule Content

Total Structure Weight: 209.29 kDa
Atom Count: 14,104
Modelled Residue Count: 1,927
Deposited Residue Count: 1,964
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Xylulokinase	A, B, C, D	491	Brucella ovis ATCC 25840	Mutation(s): 0 Gene Names: xylB, BOV_0550 EC: 2.7.1.17
UniProt
Find proteins for A0A0H3APL8 (Brucella ovis (strain ATCC 25840 / 63/290 / NCTC 10512)) Explore A0A0H3APL8 Go to UniProtKB: A0A0H3APL8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0H3APL8
Sequence Annotations Expand
Reference Sequence LOADING

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free: 0.230 (Depositor), 0.230 (DCC)
R-Value Work: 0.166 (Depositor), 0.170 (DCC)
R-Value Observed: 0.169 (Depositor)

Diffraction Data: https://doi.org/10.18430/M35VM1

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.66	α = 90
b = 167.07	β = 101.61
c = 117.83	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2017-05-10

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2017-05-10
Type: Initial release
Version 1.1: 2023-10-04
Changes: Data collection, Database references, Refinement description

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.