3R0D | pdb_00003r0d

Crystal structure of Cytosine Deaminase from Escherichia Coli complexed with two zinc atoms in the active site

• PDB DOI: https://doi.org/10.2210/pdb3R0D/pdb

• Classification: HYDROLASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-03-07 Released: 2012-03-07 
• Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Kamat, S., Hitchcock, D., Raushel, F.M., Almo, S.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.213 (Depositor), 0.207 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.191 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Cytosine Deaminase from Escherichia Coli complexed with two zinc atoms in the active site

Fedorov, A.A., Fedorov, E.V., Kamat, S., Hitchcock, D., Raushel, F.M., Almo, S.C.

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 48.39 kDa 
• Atom Count: 3,610 
• Modeled Residue Count: 422 
• Deposited Residue Count: 427 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytosine deaminase	A	427	Escherichia coli K-12	Mutation(s): 0  Gene Names: codA, b0337, JW0328 EC: 3.5.4.1 (PDB Primary Data), 3.5.4 (UniProt)
UniProt
Find proteins for P25524 (Escherichia coli (strain K12)) Explore P25524  Go to UniProtKB:  P25524

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PXN	B [auth A]	(2S)-1-[3-{[(2R)-2-hydroxypropyl]oxy}-2,2-bis({[(2R)-2-hydroxypropyl]oxy}methyl)propoxy]propan-2-ol C17 H36 O8 GXEZGLLPFFKHGE-FPCVCCKLSA-N
GOL	F [auth A], G [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	C [auth A], D [auth A], E [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.213 (Depositor), 0.207 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.191 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 145.492	α = 90
b = 145.492	β = 90
c = 199.704	γ = 120

Software Package:

Software Name	Purpose
ADSC	data collection
BALBES	phasing
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-03-07 
Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Kamat, S., Hitchcock, D., Raushel, F.M., Almo, S.C.

Revision History  

• Version 1.0: 2012-03-07
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description