4IZU | pdb_00004izu

The E41Q mutant of the amidase from Nesterenkonia sp. AN1 showing the result of Michael addition of acrylamide at the active site cysteine

PDB DOI: https://doi.org/10.2210/pdb4IZU/pdb

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

Deposited: 2013-01-30 Released: 2014-02-12
Deposition Author(s): Kimani, S.W., Sewell, B.T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free:
0.199 (Depositor), 0.198 (DCC)
R-Value Work:
0.173 (Depositor), 0.172 (DCC)
R-Value Observed:
0.174 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 4IZU

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

Literature

Covalent modifications of the active site cysteine occur as a result of mutating the glutamate of the catalytic triad in the amidase from Nesterenkonia sp.

Kimani, S.W., Hunter, R., Vlok, M., Watermeyer, J., Sewell, B.T.

To be published.

Macromolecule Content

Total Structure Weight: 30.32 kDa
Atom Count: 2,301
Modeled Residue Count: 254
Deposited Residue Count: 283
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ROP Query on ROP Download:Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A]	B [auth A], C [auth A]	PROPIONAMIDE C₃ H₇ N O QLNJFJADRCOGBJ-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]
1HC Query on 1HC Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	prop-2-enamide C₃ H₅ N O HRPVXLWXLXDGHG-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.199 (Depositor), 0.198 (DCC)
R-Value Work: 0.173 (Depositor), 0.172 (DCC)
R-Value Observed: 0.174 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.102	α = 90
b = 115.452	β = 90
c = 65.933	γ = 90

Software Package:

Software Name	Purpose
d*TREK	data scaling
d*TREK	data reduction
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2014-02-12

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-02-12
Type: Initial release
Version 1.1: 2014-02-19
Changes: Other
Version 1.2: 2024-11-27
Changes: Data collection, Database references, Derived calculations, Structure summary

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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.