5NYC | pdb_00005nyc

A C145A mutant of Nesterenkonia AN1 amidase bound to propionitrile

• PDB DOI: https://doi.org/10.2210/pdb5NYC/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: 1.51 Å
• R-Value Free: 
  0.171 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.144 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.145 (Depositor) 

Starting Model: experimental

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 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 30.45 kDa 
• Atom Count: 2,224 
• 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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	B [auth A], C [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
CNV	D [auth A], E [auth A], F [auth A]	propanenitrile C3 H5 N FVSKHRXBFJPNKK-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.51 Å
• R-Value Free:  0.171 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.144 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.145 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.469	α = 90
b = 115.492	β = 90
c = 65.192	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
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 1.1: 2024-01-17
  Changes: Data collection, Database references, Derived calculations, Refinement description