2OB3 | pdb_00002ob3

Structure of Phosphotriesterase mutant H257Y/L303T

PDB DOI: https://doi.org/10.2210/pdb2OB3/pdb

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

Deposited: 2006-12-18 Released: 2007-01-30
Deposition Author(s): Kim, J., Ramagopal, U.A., Tsai, P., Raushel, F.M., Almo, S.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.04 Å
R-Value Free:
0.127 (Depositor)
R-Value Work:
0.105 (Depositor)
R-Value Observed:
0.105 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 2OB3

This is version 1.6 of the entry. See complete history.

Literature

Structure of Phosphotriesterase mutant H257Y/L303T

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

To be published.

Macromolecule Content

Total Structure Weight: 72.45 kDa
Atom Count: 6,065
Modeled Residue Count: 660
Deposited Residue Count: 660
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Parathion hydrolase	A, B	330	Brevundimonas diminuta	Mutation(s): 2 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A434
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BTB Query on BTB Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B]	E [auth A], H [auth B]	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₈ H₁₉ N O₅ OWMVSZAMULFTJU-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Interactions & Density Focus chain E [auth A] Focus chain H [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth B] SDF format, chain G [auth B] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth B] MOL2 format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain F [auth B] mmCIF format, chain G [auth B] mmCIF format, chain D [auth A]	C [auth A], D [auth A], F [auth B], G [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain F [auth B] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain F [auth B] Focus chain G [auth B]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.04 Å
R-Value Free: 0.127 (Depositor)
R-Value Work: 0.105 (Depositor)
R-Value Observed: 0.105 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.362	α = 104.86
b = 45.374	β = 93.27
c = 79.211	γ = 97.81

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2007-01-30

Deposition Author(s):

Ramagopal, U.A.

Revision History (Full details and data files)

Version 1.0: 2007-01-30
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2017-10-18
Changes: Refinement description
Version 1.4: 2021-10-20
Changes: Database references, Derived calculations
Version 1.5: 2023-08-30
Changes: Data collection, Refinement description
Version 1.6: 2023-11-15
Changes: Data collection

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