2OPA | pdb_00002opa

YwhB binary complex with 2-Fluoro-p-hydroxycinnamate

PDB DOI: https://doi.org/10.2210/pdb2OPA/pdb

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

Deposited: 2007-01-28 Released: 2008-02-05
Deposition Author(s): Hackert, M.L., Whitman, C.P., Almrud, J.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.249 (Depositor), 0.241 (DCC)
R-Value Work:
0.217 (Depositor), 0.203 (DCC)

Starting Model: experimental
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Ligand Structure Quality Assessment

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: 14.23 kDa
Atom Count: 1,020
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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FHC Query on FHC Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	2-FLUORO-3-(4-HYDROXYPHENYL)-2E-PROPENEOATE C₉ H₆ F O₃ SBIZDOWXYPNTOJ-VMPITWQZSA-M		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.249 (Depositor), 0.241 (DCC)
R-Value Work: 0.217 (Depositor), 0.203 (DCC)

Space Group: I 4 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 141.339	α = 90
b = 141.339	β = 90
c = 141.339	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
CNS	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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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: 2017-10-18
Changes: Advisory, Refinement description
Version 1.3: 2023-08-30
Changes: Advisory, 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.