2FPN | pdb_00002fpn

The crystal structure of the ywmB protein from Bacillus subtilis

• PDB DOI: https://doi.org/10.2210/pdb2FPN/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Bacillus subtilis
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2006-01-16 Released: 2006-03-14 
• Deposition Author(s): Zhang, R., Wu, R., Moy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.49 Å
• R-Value Free: 
  0.281 (Depositor), 0.278 (DCC) 
• R-Value Work: 
  0.242 (Depositor) 
• R-Value Observed: 
  0.244 (Depositor) 

Literature

The crystal structure of the ywmB protein from Bacillus subtilis

Zhang, R., Wu, R., Moy, S., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content 

• Total Structure Weight: 25.69 kDa 
• Atom Count: 1,753 
• Modeled Residue Count: 205 
• Deposited Residue Count: 216 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ywmB	A	216	Bacillus subtilis	Mutation(s): 8  Gene Names: ywmB
UniProt
Find proteins for O32277 (Bacillus subtilis (strain 168)) Explore O32277  Go to UniProtKB:  O32277

Small Molecules

Modified Residues  1 Unique
ID	Chains	Modified Residue	Modification Type	Formula	2D Diagram
MSE	A	MET	Selenomethionine	C5 H11 N O2 Se

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.49 Å
• R-Value Free:  0.281 (Depositor), 0.278 (DCC) 
• R-Value Work:  0.242 (Depositor) 
• R-Value Observed: 0.244 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.79	α = 90
b = 50.856	β = 96.49
c = 81.259	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-03-14 
Deposition Author(s): Zhang, R., Wu, R., Moy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2006-03-14
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Derived calculations, Version format compliance
• Version 1.3: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Structure summary