3OCQ | pdb_00003ocq

crystal structure of tRNA-specific Adenosine deaminase from Salmonella enterica

• PDB DOI: https://doi.org/10.2210/pdb3OCQ/pdb

• Classification: HYDROLASE
• Organism(s): Salmonella enterica
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-08-10 Released: 2010-08-18 
• Deposition Author(s): Kim, J., Ramagopal, U.A., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 
  0.238 (Depositor), 0.235 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.189 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of tRNA-specific Adenosine deaminase from Salmonella enterica

Kim, J., Ramagopal, U.A., Burley, S.K., Almo, S.C.

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 (software)

Macromolecule Content 

• Total Structure Weight: 20.39 kDa 
• Atom Count: 1,179 
• Modeled Residue Count: 146 
• Deposited Residue Count: 183 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative Cytosine/adenosine deaminase	A	183	Salmonella enterica	Mutation(s): 0  Gene Names: SCH_2563, yfhC EC: 3.5.4.4 (PDB Primary Data), 3.5.4.33 (UniProt)
UniProt
Find proteins for Q57LE3 (Salmonella choleraesuis (strain SC-B67)) Explore Q57LE3  Go to UniProtKB:  Q57LE3

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free:  0.238 (Depositor), 0.235 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: P 3 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.49	α = 90
b = 75.49	β = 90
c = 44.757	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-08-18 
Deposition Author(s): Kim, J., Ramagopal, U.A., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2010-08-18
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Refinement description