1R0U | pdb_00001r0u

Crystal structure of ywiB protein from Bacillus subtilis

PDB DOI: https://doi.org/10.2210/pdb1R0U/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Bacillus subtilis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2003-09-23 Released: 2003-12-30
Deposition Author(s): Osipiuk, J., Xu, X., Savchenko, A., Edwards, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free:
0.212 (Depositor), 0.199 (DCC)
R-Value Work:
0.185 (Depositor), 0.196 (DCC)
R-Value Observed:
0.185 (Depositor)

wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of ywiB protein from Bacillus subtilis

Osipiuk, J., Xu, X., Savchenko, A., Edwards, A., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 16.88 kDa
Atom Count: 1,435
Modeled Residue Count: 142
Deposited Residue Count: 148
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
protein ywiB	A	148	Bacillus subtilis	Mutation(s): 0 Gene Names: ywiB
UniProt
Find proteins for O07624 (Bacillus subtilis (strain 168)) Explore O07624 Go to UniProtKB: O07624
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O07624
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL 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]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-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: 1.75 Å
R-Value Free: 0.212 (Depositor), 0.199 (DCC)
R-Value Work: 0.185 (Depositor), 0.196 (DCC)
R-Value Observed: 0.185 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.428	α = 90
b = 48.428	β = 90
c = 136.156	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
CNS	phasing
SOLVE	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2003-12-30

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2003-12-30
Type: Initial release
Version 1.1: 2008-04-29
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.3: 2024-02-14
Changes: Advisory, Data collection, Database references, Derived calculations

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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.