5NZ5 | pdb_00005nz5

A C145S mutant of Nesterenkonia AN1 amidase from the nitrilase superfamily

PDB DOI: https://doi.org/10.2210/pdb5NZ5/pdb

Classification: HYDROLASE
Organism(s): Nesterenkonia sp. 10004
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2017-05-12 Released: 2018-06-13
Deposition Author(s): Kimani, S.W., Sewell, B.T.
Funding Organization(s): National Research Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.47 Å
R-Value Free:
0.163 (Depositor), 0.164 (DCC)
R-Value Work:
0.141 (Depositor), 0.142 (DCC)
R-Value Observed:
0.142 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 5NZ5

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

Literature

Substrate recognition by an amidase of the nitrilase superfamily

Kimani, S.W., Venter, G.A., Sewell, B.T.

To be published.

Macromolecule Content

Total Structure Weight: 30.08 kDa
Atom Count: 2,228
Modeled Residue Count: 259
Deposited Residue Count: 283
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Amidase	A	283	Nesterenkonia sp. 10004	Mutation(s): 1 Gene Names: Nit2 EC: 3.5.1.4
UniProt
Find proteins for D0VWZ1 (Nesterenkonia sp. 10004) Explore D0VWZ1 Go to UniProtKB: D0VWZ1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D0VWZ1
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.47 Å
R-Value Free: 0.163 (Depositor), 0.164 (DCC)
R-Value Work: 0.141 (Depositor), 0.142 (DCC)
R-Value Observed: 0.142 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.399	α = 90
b = 114.996	β = 90
c = 65.589	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
PHASER	phasing
MOSFLM	data reduction

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2018-06-13

Deposition Author(s):

Funding Organization	Location	Grant Number
National Research Foundation	South Africa	91532

Revision History (Full details and data files)

Version 1.0: 2018-06-13
Type: Initial release
Version 1.1: 2024-01-17
Changes: Data collection, Database references, Refinement description

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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.