2O4M | pdb_00002o4m

Structure of Phosphotriesterase mutant I106G/F132G/H257Y

• PDB DOI: https://doi.org/10.2210/pdb2O4M/pdb

• Classification: HYDROLASE
• Organism(s): Brevundimonas diminuta
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2006-12-04 Released: 2007-12-18 
• Deposition Author(s): Kim, J., Ramagopal, U.A., Tsai, P., Raushel, F.M., Almo, S.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.64 Å
• R-Value Free: 
  0.244 (Depositor), 0.241 (DCC) 
• R-Value Work: 
  0.189 (Depositor), 0.187 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

Starting Model: experimental

Literature

Structure of Phosphotriesterase mutant I106G/F132G/H257Y

Kim, J., Ramagopal, U.A., Tsai, P., Raushel, F.M., 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.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 145.93 kDa 
• Atom Count: 11,956 
• Modeled Residue Count: 1,323 
• Deposited Residue Count: 1,324 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Parathion hydrolase	A, B, C, D [auth P]	331	Brevundimonas diminuta	Mutation(s): 3  Gene Names: opd EC: 3.1.8.1
UniProt
Find proteins for P0A434 (Brevundimonas diminuta) Explore P0A434  Go to UniProtKB:  P0A434

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CAC	AA [auth C], K [auth A], KA [auth P], R [auth B]	CACODYLATE ION C2 H6 As O2 OGGXGZAMXPVRFZ-UHFFFAOYSA-M
GOL	BA [auth C], CA [auth C], LA [auth P], MA [auth P], S [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	E [auth A], EA [auth P], F [auth A], FA [auth P], G [auth A], GA [auth P], H [auth A], HA [auth P], I [auth A], IA [auth P], J [auth A], JA [auth P], M [auth B], N [auth B], O [auth B], P [auth B], Q [auth B], U [auth C], V [auth C], W [auth C], X [auth C], Y [auth C], Z [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACY	DA [auth C], L [auth A], T [auth B]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
KCX	A, B, C, D [auth P]	L-PEPTIDE LINKING	C7 H14 N2 O4		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.64 Å
• R-Value Free:  0.244 (Depositor), 0.241 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.187 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.759	α = 90.03
b = 68.906	β = 100.29
c = 89.67	γ = 94.12

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-12-18 
Deposition Author(s): Kim, J., Ramagopal, U.A., Tsai, P., Raushel, F.M., Almo, S.C.

Revision History  

• Version 1.0: 2007-12-18
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2017-10-18
  Changes: Refinement description
• Version 1.3: 2021-10-20
  Changes: Database references, Derived calculations
• Version 1.4: 2023-08-30
  Changes: Data collection, Refinement description
• Version 1.5: 2023-11-15
  Changes: Data collection