5NXZ | pdb_00005nxz

A C145A mutant of Nesterenkonia AN1 amidase from the nitrilase superfamily

• PDB DOI: https://doi.org/10.2210/pdb5NXZ/pdb

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


• Deposited: 2017-05-11 Released: 2018-05-30 
• Deposition Author(s): Kimani, S.W., Sewell, B.T.
• Funding Organization(s): National Research Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.21 Å
• R-Value Free: 
  0.196 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.168 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.169 (Depositor) 

Starting Model: other

Literature

Substrate recognition by an amidase of the nitrilase superfamily

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

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 30.07 kDa 
• Atom Count: 2,204 
• Modeled Residue Count: 261 
• Deposited Residue Count: 283 
• Unique protein chains: 1

Macromolecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.21 Å
• R-Value Free:  0.196 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.168 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.169 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.814	α = 90
b = 114.977	β = 90
c = 65.827	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-05-30 
Deposition Author(s): Kimani, S.W., Sewell, B.T.

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Funding Organization	Location	Grant Number
National Research Foundation	South Africa	91532

Revision History  

• Version 1.0: 2018-05-30
  Type: Initial release
  
• Version 2.0: 2024-05-01
  Changes: Atomic model, Data collection, Database references, Refinement description