5JQN | pdb_00005jqn

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.19 Å
R-Value Free:
0.183 (Depositor), 0.180 (DCC)
R-Value Work:
0.175 (Depositor), 0.180 (DCC)
R-Value Observed:
0.175 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSD Query on 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 (Depositor), 0.180 (DCC)
R-Value Work: 0.175 (Depositor), 0.180 (DCC)
R-Value Observed: 0.175 (Depositor)

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

View Full Validation Report

Entry History

Deposition Data

Released Date: 2016-05-18

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-05-18
Type: Initial release
Version 1.1: 2024-01-10
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-11-20
Changes: Structure summary

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.