6FS3 | pdb_00006fs3

Phosphotriesterase PTE_A53_1

PDB DOI: https://doi.org/10.2210/pdb6FS3/pdb

Classification: HYDROLASE
Organism(s): Brevundimonas diminuta
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2018-02-19 Released: 2019-03-20
Deposition Author(s): Dym, O., Aggarwal, N., Albeck, S., Unger, T., Hamer Rogotner, S., Silman, I., Leader, H., Ashani, Y., Goldsmith, M., Greisen, P., Tawfik, D., Sussman, L.J.
Funding Organization(s): DTRA

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free:
0.201 (Depositor), 0.200 (DCC)
R-Value Work:
0.167 (Depositor), 0.167 (DCC)
R-Value Observed:
0.169 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Crystal structures of Bacterail Phosphotriesterase variant with high catalytic activity towards organophosphate nerve agents developed by use of structure-based design and molecular evolution

Dym, O., Aggarwal, N., Sussman, J.L., Silman, I.

To be published.

Macromolecule Content

Total Structure Weight: 73.93 kDa
Atom Count: 5,518
Modeled Residue Count: 658
Deposited Residue Count: 678
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Parathion hydrolase	A, B	339	Brevundimonas diminuta	Mutation(s): 0 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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
9ON Query on 9ON Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain F [auth A] MOL2 format, chain J [auth B] MOL2 format, chain F [auth A] mmCIF format, chain J [auth B] mmCIF format, chain F [auth A]	F [auth A], J [auth B]	(2~{S})-2-methylpentanedioic acid C₆ H₁₀ O₄ AQYCMVICBNBXNA-BYPYZUCNSA-N		Interactions Focus chain F [auth A] Focus chain J [auth B] Interactions & Density Focus chain F [auth A] Focus chain J [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A], H [auth B], I [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth B]
FMT Query on FMT Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain C [auth A] MOL2 format, chain G [auth B] MOL2 format, chain C [auth A] mmCIF format, chain G [auth B] mmCIF format, chain C [auth A]	C [auth A], G [auth B]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.201 (Depositor), 0.200 (DCC)
R-Value Work: 0.167 (Depositor), 0.167 (DCC)
R-Value Observed: 0.169 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.469	α = 90
b = 81.46	β = 95.12
c = 70.71	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2019-03-20

Deposition Author(s):

Funding Organization	Location	Grant Number
DTRA	United States	HDTRA1-11-C-0026).
DTRA	United States	CB10265 / HDTRA1724528

Revision History (Full details and data files)

Version 1.0: 2019-03-20
Type: Initial release
Version 1.1: 2024-01-17
Changes: Data collection, Database references, Derived calculations, Refinement description

6FS3 | pdb_00006fs3

Phosphotriesterase PTE_A53_1

Literature

Crystal structures of Bacterail Phosphotriesterase variant with high catalytic activity towards organophosphate nerve agents developed by use of structure-based design and molecular evolution

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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