5IFZ | pdb_00005ifz

Crystal Structure of Ribose-5-phosphate Isomerase from Brucella melitensis 16M

PDB DOI: https://doi.org/10.2210/pdb5IFZ/pdb

Classification: ISOMERASE
Organism(s): Brucella melitensis bv. 1 str. 16M
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2016-02-26 Released: 2016-04-13
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:
0.211 (Depositor), 0.210 (DCC)
R-Value Work:
0.181 (Depositor), 0.181 (DCC)
R-Value Observed:
0.183 (Depositor)

Starting Model: experimental
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This is version 1.1 of the entry. See complete history.

Literature

Crystal Structure of Ribose-5-phosphate Isomerase from Brucella melitensis 16M

Delker, S.L., Dranow, D.M., Abendroth, J., Lorimer, D., Edwards, T.E.

To be published.

Macromolecule Content

Total Structure Weight: 36.45 kDa
Atom Count: 1,816
Modeled Residue Count: 235
Deposited Residue Count: 344
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribose 5-phosphate isomerase	A, B	172	Brucella melitensis bv. 1 str. 16M	Mutation(s): 0 Gene Names: BMEII0424 EC: 5.3.1.6
UniProt
Find proteins for Q8YCV4 (Brucella melitensis biotype 1 (strain ATCC 23456 / CCUG 17765 / NCTC 10094 / 16M)) Explore Q8YCV4 Go to UniProtKB: Q8YCV4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8YCV4
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.211 (Depositor), 0.210 (DCC)
R-Value Work: 0.181 (Depositor), 0.181 (DCC)
R-Value Observed: 0.183 (Depositor)

Diffraction Data:

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.57	α = 90
b = 51.57	β = 90
c = 177.29	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2016-04-13

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2016-04-13
Type: Initial release
Version 1.1: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description

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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.