2OTN | pdb_00002otn

Crystal structure of the catalytically active form of diaminopimelate epimerase from Bacillus anthracis

• PDB DOI: https://doi.org/10.2210/pdb2OTN/pdb

• Classification: ISOMERASE
• Organism(s): Bacillus anthracis str. Ames
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-02-08 Released: 2008-03-04 
• Deposition Author(s): Matho, M.H., Fukuda, K., Santelli, E., Jaroszewski, L., Liddington, R.C., Roper, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.250 (Depositor), 0.253 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.183 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Starting Model: experimental

Literature

Crystal structure and inhibition of a catalytically active form of diaminopimelate epimerase (DapF)from Bacillus anthracis

Matho, M.H., Fukuda, K., Lloyd, A.J., Santelli, E., Jaroszewski, L., Scott, D.J., Liddington, R.C., Roper, D.

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.

Macromolecule Content 

• Total Structure Weight: 67.63 kDa 
• Atom Count: 4,710 
• Modeled Residue Count: 581 
• Deposited Residue Count: 616 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Diaminopimelate epimerase	A, B	308	Bacillus anthracis str. Ames	Mutation(s): 0  Gene Names: dapF EC: 5.1.1.7
UniProt
Find proteins for Q81XR2 (Bacillus anthracis) Explore Q81XR2  Go to UniProtKB:  Q81XR2

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.250 (Depositor), 0.253 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.183 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.863	α = 90
b = 87.334	β = 90
c = 110.453	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-03-04 
Deposition Author(s): Matho, M.H., Fukuda, K., Santelli, E., Jaroszewski, L., Liddington, R.C., Roper, D.

Revision History  

• Version 1.0: 2008-03-04
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Source and taxonomy, Version format compliance
• Version 1.2: 2023-08-30
  Changes: Data collection, Database references, Refinement description