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.

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
View more details

wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

Structure of Phosphotriesterase mutant I106G/F132G/H257Y

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

To be published.

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

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0A434
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CAC Query on CAC Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain K [auth A] SDF format, chain KA [auth P] SDF format, chain R [auth B] MOL2 format, chain AA [auth C] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth P] MOL2 format, chain R [auth B] mmCIF format, chain AA [auth C] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth P] mmCIF format, chain R [auth B]	AA [auth C], K [auth A], KA [auth P], R [auth B]	CACODYLATE ION C₂ H₆ As O₂ OGGXGZAMXPVRFZ-UHFFFAOYSA-M		Interactions Focus chain AA [auth C] Focus chain K [auth A] Focus chain KA [auth P] Focus chain R [auth B] Interactions & Density Focus chain AA [auth C] Focus chain K [auth A] Focus chain KA [auth P] Focus chain R [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain CA [auth C] SDF format, chain LA [auth P] SDF format, chain MA [auth P] SDF format, chain S [auth B] MOL2 format, chain BA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain LA [auth P] MOL2 format, chain MA [auth P] MOL2 format, chain S [auth B] mmCIF format, chain BA [auth C] mmCIF format, chain CA [auth C] mmCIF format, chain LA [auth P] mmCIF format, chain MA [auth P] mmCIF format, chain S [auth B]	BA [auth C], CA [auth C], LA [auth P], MA [auth P], S [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain BA [auth C] Focus chain CA [auth C] Focus chain LA [auth P] Focus chain MA [auth P] Focus chain S [auth B] Interactions & Density Focus chain BA [auth C] Focus chain CA [auth C] Focus chain LA [auth P] Focus chain MA [auth P] Focus chain S [auth B]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain EA [auth P] SDF format, chain F [auth A] SDF format, chain FA [auth P] SDF format, chain G [auth A] SDF format, chain GA [auth P] SDF format, chain H [auth A] SDF format, chain HA [auth P] SDF format, chain I [auth A] SDF format, chain IA [auth P] SDF format, chain J [auth A] SDF format, chain JA [auth P] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain U [auth C] SDF format, chain V [auth C] SDF format, chain W [auth C] SDF format, chain X [auth C] SDF format, chain Y [auth C] SDF format, chain Z [auth C] MOL2 format, chain E [auth A] MOL2 format, chain EA [auth P] MOL2 format, chain F [auth A] MOL2 format, chain FA [auth P] MOL2 format, chain G [auth A] MOL2 format, chain GA [auth P] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth P] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth P] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth P] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth C] mmCIF format, chain E [auth A] mmCIF format, chain EA [auth P] mmCIF format, chain F [auth A] mmCIF format, chain FA [auth P] mmCIF format, chain G [auth A] mmCIF format, chain GA [auth P] mmCIF format, chain H [auth A] mmCIF format, chain HA [auth P] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth P] mmCIF format, chain J [auth A] mmCIF format, chain JA [auth P] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain U [auth C] mmCIF format, chain V [auth C] mmCIF format, chain W [auth C] mmCIF format, chain X [auth C] mmCIF format, chain Y [auth C] mmCIF format, chain Z [auth C]	E [auth A] EA [auth P] F [auth A] FA [auth P] G [auth A] 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		Interactions Focus chain E [auth A] Focus chain EA [auth P] Focus chain F [auth A] Focus chain FA [auth P] Focus chain G [auth A] Focus chain GA [auth P] Focus chain H [auth A] Focus chain HA [auth P] Focus chain I [auth A] Focus chain IA [auth P] Focus chain J [auth A] Focus chain JA [auth P] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain E [auth A] Focus chain EA [auth P] Focus chain F [auth A] Focus chain FA [auth P] Focus chain G [auth A] Focus chain GA [auth P] Focus chain H [auth A] Focus chain HA [auth P] Focus chain I [auth A] Focus chain IA [auth P] Focus chain J [auth A] Focus chain JA [auth P] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C]
ACY Query on ACY Download Ideal Coordinates CCD File SDF format, chain DA [auth C] SDF format, chain L [auth A] SDF format, chain T [auth B] MOL2 format, chain DA [auth C] MOL2 format, chain L [auth A] MOL2 format, chain T [auth B] mmCIF format, chain DA [auth C] mmCIF format, chain L [auth A] mmCIF format, chain T [auth B]	DA [auth C], L [auth A], T [auth B]	ACETIC ACID C₂ H₄ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-N		Interactions Focus chain DA [auth C] Focus chain L [auth A] Focus chain T [auth B] Interactions & Density Focus chain DA [auth C] Focus chain L [auth A] Focus chain T [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
KCX Query on 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

View Full Validation Report

Entry History

Deposition Data

Released Date: 2007-12-18

Deposition Author(s):

Revision History (Full details and data files)

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