2D30 | pdb_00002d30

Crystal Structure of Cytidine Deaminase Cdd-2 (BA4525) from Bacillus Anthracis at 2.40A Resolution

• PDB DOI: https://doi.org/10.2210/pdb2D30/pdb

• Classification: HYDROLASE
• Organism(s): Bacillus anthracis
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2005-09-21 Released: 2006-09-19 
• Deposition Author(s): Levdikov, V.M., Blagova, E.V., Fogg, M.J., Brannigan, J.A., Moroz, O.V., Wilkinson, A.J., Wilson, K.S., Structural Proteomics in Europe (SPINE)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.251 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.164 (Depositor), 0.173 (DCC) 
• R-Value Observed: 
  0.168 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Cytidine Deaminase Cdd-2 (BA4525) from Bacillus Anthracis at 2.40A Resolution

Levdikov, V.M., Blagova, E.V., Fogg, M.J., Brannigan, J.A., Moroz, O.V., Wilkinson, A.J., Wilson, K.S.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 31.13 kDa 
• Atom Count: 2,017 
• Modeled Residue Count: 248 
• Deposited Residue Count: 282 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
cytidine deaminase	A, B	141	Bacillus anthracis	Mutation(s): 0  Gene Names: cdd-2 EC: 3.5.4.5
UniProt
Find proteins for A0A6L7GZQ8 (Bacillus anthracis) Explore A0A6L7GZQ8  Go to UniProtKB:  A0A6L7GZQ8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A], D [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.251 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.164 (Depositor), 0.173 (DCC) 
• R-Value Observed: 0.168 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.792	α = 90
b = 50.552	β = 132.1
c = 70.438	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-09-19 
Deposition Author(s): Levdikov, V.M., Blagova, E.V., Fogg, M.J., Brannigan, J.A., Moroz, O.V., Wilkinson, A.J., Wilson, K.S., Structural Proteomics in Europe (SPINE)

Revision History  

• Version 1.0: 2006-09-19
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description