5MKD | pdb_00005mkd

Crystal structure of Bacillus subtilis Ywea

• PDB DOI: https://doi.org/10.2210/pdb5MKD/pdb

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


• Deposited: 2016-12-03 Released: 2017-01-25 
• Deposition Author(s): Carrington, J., van Aalten, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.51 Å
• R-Value Free: 
  0.263 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.208 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

Literature

Crystal structure of Bacillus subtilis Ywea

Carrington, J., van Aalten, D.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 54.18 kDa 
• Atom Count: 3,830 
• Modeled Residue Count: 494 
• Deposited Residue Count: 496 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ywea	A, B, C, D	124	Bacillus subtilis	Mutation(s): 0  Gene Names: B4417_2102
UniProt
Find proteins for P39632 (Bacillus subtilis (strain 168)) Explore P39632  Go to UniProtKB:  P39632

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.51 Å
• R-Value Free:  0.263 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.208 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: C 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.405	α = 90
b = 128.306	β = 90
c = 84.327	γ = 90

Software Package:

Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MOLREP	phasing
xia2	data reduction
xia2	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-01-25 
Deposition Author(s): Carrington, J., van Aalten, D.

Revision History  

• Version 1.0: 2017-01-25
  Type: Initial release
  
• Version 1.1: 2024-05-08
  Changes: Data collection, Database references