1R0U

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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.212 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.185 (Depositor) 

Literature

Crystal structure of ywiB protein from Bacillus subtilis

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

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

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

Macromolecules

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.212 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.200 (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

Entry History 

Deposition Data

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

Revision History  

• 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