2OP8 | pdb_00002op8

Crystal Structure of YwhB- Homologue of 4-Oxalocrotonate Tautomerase

PDB DOI: https://doi.org/10.2210/pdb2OP8/pdb

Classification: ISOMERASE
Organism(s): Bacillus subtilis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2007-01-27 Released: 2008-02-05
Deposition Author(s): Hackert, M.L., Whitman, C.P., Almrud, J.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.237 (Depositor), 0.239 (DCC)
R-Value Work:
0.218 (Depositor), 0.220 (DCC)
R-Value Observed:
0.218 (Depositor)

Starting Model: experimental
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This is version 1.3 of the entry. See complete history.

Literature

The Crystal Structure of YwhB, a 4-Oxalocrotonate Tautomerase Homologue from Bacillus subtilis: The Structural Basis for Catalysis, Inhibition, and Reaction Stereoselectivity

Hackert, M.L., Whitman, C.P., Almrud, J.J., Dasgupta, R., Wang, S.C., Johnson, W.H.

To be published.

Macromolecule Content

Total Structure Weight: 14.05 kDa
Atom Count: 1,005
Modeled Residue Count: 122
Deposited Residue Count: 122
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable tautomerase ywhB	A, B	61	Bacillus subtilis	Mutation(s): 0 Gene Names: ywhB EC: 5.3.2 (PDB Primary Data), 5.3.2.6 (UniProt)
UniProt
Find proteins for P70994 (Bacillus subtilis (strain 168)) Explore P70994 Go to UniProtKB: P70994
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P70994
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.237 (Depositor), 0.239 (DCC)
R-Value Work: 0.218 (Depositor), 0.220 (DCC)
R-Value Observed: 0.218 (Depositor)

Space Group: I 4 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 141.8	α = 90
b = 141.8	β = 90
c = 141.8	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2008-02-05

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2008-02-05
Type: Initial release
Version 1.1: 2011-07-13
Changes: Derived calculations, Version format compliance
Version 1.2: 2018-04-04
Changes: Advisory, Data collection
Version 1.3: 2023-08-30
Changes: Advisory, Data collection, Database references, 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.