5JQN

NitN Amidase from Neterenkonia sp. AN1 after thrombin His-tag removal.

• PDB DOI: https://doi.org/10.2210/pdb5JQN/pdb

• Classification: HYDROLASE
• Organism(s): Nesterenkonia sp. AN1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-05-05 Released: 2016-05-18 
• Deposition Author(s): Sewell, B.T., Kimani, S.W., Weber, B.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.19 Å
• R-Value Free: 0.183 
• R-Value Work: 0.175 
• R-Value Observed: 0.175 

Starting Model: experimental

Literature

QM/MM Modelling of Substrate Binding in the Amidase Active Site

Sewell, B.T., Kimani, S.W., Venter, G.A., Hunter, R., Schell, D.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)

Macromolecule Content

• Total Structure Weight: 28.24 kDa 
• Atom Count: 2,184 
• Modelled Residue Count: 255 
• Deposited Residue Count: 266 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aliphatic amidase	A	266	Nesterenkonia sp. AN1	Mutation(s): 0  Gene Names: nit2 EC: 3.5.1.4
UniProt
Find proteins for C6K3Z5 (Nesterenkonia sp. AN1) Explore C6K3Z5  Go to UniProtKB:  C6K3Z5

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSD	A	L-PEPTIDE LINKING	C3 H7 N O4 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.19 Å
• R-Value Free: 0.183 
• R-Value Work: 0.175 
• R-Value Observed: 0.175 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.423	α = 90
b = 115.794	β = 90
c = 65.757	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-05-18 
Deposition Author(s): Sewell, B.T., Kimani, S.W., Weber, B.W.

Revision History  

• Version 1.0: 2016-05-18
  Type: Initial release
  
• Version 1.1: 2024-01-10
  Changes: Data collection, Database references, Refinement description