4XUK | pdb_00004xuk

Crystal structure of hydrolase AbOPH in beta lactamase superfamily

PDB DOI: https://doi.org/10.2210/pdb4XUK/pdb

Classification: HYDROLASE
Organism(s): Acinetobacter sp. NBRC 100985
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2015-01-26 Released: 2015-10-21
Deposition Author(s): Chen, J., Xu, J.H., Zhou, J.H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.238 (Depositor), 0.221 (DCC)
R-Value Work:
0.204 (Depositor), 0.196 (DCC)
R-Value Observed:
0.206 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history.

Literature

Marked enhancement of Acinetobacter sp. organophosphorus hydrolase activity by a single residue substitution Ile211Ala

Chen, J., Lu, X.J., Chen, Q., Pan, J., Zhou, J.H., Xu, J.H.

(2015) Bioresour Bioprocess

DOI: https://doi.org/10.1186/s40643-015-0067-3

Macromolecule Content

Total Structure Weight: 64.83 kDa
Atom Count: 5,003
Modeled Residue Count: 582
Deposited Residue Count: 582
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative hydrolase	A, B	291	Acinetobacter sp. NBRC 100985	Mutation(s): 2 Gene Names: ACT4_021_01090
UniProt
Find proteins for N8ZXR1 (Acinetobacter venetianus (strain ATCC 31012 / DSM 23050 / BCRC 14357 / CCUG 45561 / CIP 110063 / KCTC 2702 / LMG 19082 / RAG-1)) Explore N8ZXR1 Go to UniProtKB: N8ZXR1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	N8ZXR1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain E [auth B] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain F [auth B] MOL2 format, chain E [auth B] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain F [auth B] mmCIF format, chain E [auth B] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], E [auth B], F [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.238 (Depositor), 0.221 (DCC)
R-Value Work: 0.204 (Depositor), 0.196 (DCC)
R-Value Observed: 0.206 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.812	α = 90
b = 82.735	β = 90
c = 99.767	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHASER	phasing
HKL-2000	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2015-10-21

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-10-21
Type: Initial release
Version 1.1: 2022-12-14
Changes: Database references, Derived calculations
Version 1.2: 2023-11-29
Changes: Data collection, Refinement description
Version 1.3: 2024-10-16
Changes: Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.