2ZC1 | pdb_00002zc1

Organophosphorus Hydrolase from Deinococcus radiodurans

• PDB DOI: https://doi.org/10.2210/pdb2ZC1/pdb

• Classification: HYDROLASE
• Organism(s): Deinococcus radiodurans
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-11-02 Released: 2008-11-25 
• Deposition Author(s): Larsen, S.D., Hawwa, R., Ratia, K., Santarsiero, B.D., Mesecar, A.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.212 (Depositor), 0.212 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.182 (DCC) 
• R-Value Observed: 
  0.182 (Depositor) 

Literature

X-Ray Structural Insights into a Phosphotriesterase

Larsen, S.D., Hawwa, R., Ratia, K., Santarsiero, B.D., Mesecar, A.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: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 36.23 kDa 
• Atom Count: 2,994 
• Modeled Residue Count: 333 
• Deposited Residue Count: 333 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphotriesterase	A	333	Deinococcus radiodurans	Mutation(s): 0  EC: 3.1.8.1
UniProt
Find proteins for Q9RVU2 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)) Explore Q9RVU2  Go to UniProtKB:  Q9RVU2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BR	B [auth A], C [auth A], D [auth A], E [auth A]	BROMIDE ION Br CPELXLSAUQHCOX-UHFFFAOYSA-M
CO	F [auth A], G [auth A]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
KCX	A	L-PEPTIDE LINKING	C7 H14 N2 O4		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.212 (Depositor), 0.212 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.182 (DCC) 
• R-Value Observed: 0.182 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.843	α = 90
b = 60.843	β = 90
c = 207.694	γ = 120

Software Package:

Software Name	Purpose
SOLVE	phasing
CNS	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-11-25 
Deposition Author(s): Larsen, S.D., Hawwa, R., Ratia, K., Santarsiero, B.D., Mesecar, A.D.

Revision History  

• Version 1.0: 2008-11-25
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2025-03-26
  Changes: Data collection, Database references, Derived calculations, Structure summary