7QOY | pdb_00007qoy

A mutant of the nitrile hydratase from Geobacillus pallidus having enhanced thermostability

PDB DOI: https://doi.org/10.2210/pdb7QOY/pdb

Classification: LYASE
Organism(s): Aeribacillus pallidus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2021-12-29 Released: 2023-01-18
Deposition Author(s): Van Wyk, J.C., Cowan, D.A., Danson, M.J., Tsekoa, T.L., Sayed, M.F., Sewell, B.T.
Funding Organization(s): National Research Foundation in South Africa

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free:
0.184 (Depositor), 0.309 (DCC)
R-Value Work:
0.142 (Depositor), 0.290 (DCC)
R-Value Observed:
0.144 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7QOY

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

Literature

A mutant of the nitrile hydratase from Geobacillus pallidus having enhanced thermostability

Van Wyk, J.C., Cowan, D.A., Danson, M.J., Tsekoa, T.L., Sayed, M.F., Sewell, B.T.

To be published.

Macromolecule Content

Total Structure Weight: 51.43 kDa
Atom Count: 3,998
Modeled Residue Count: 429
Deposited Residue Count: 445
Unique protein chains: 2

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nitrile hydratase	A	216	Aeribacillus pallidus	Mutation(s): 1 EC: 4.2.1.84
UniProt
Find proteins for Q84FS5 (Bacillus sp. RAPc8) Explore Q84FS5 Go to UniProtKB: Q84FS5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q84FS5
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nitrile hydratase subunit beta	B	229	Aeribacillus pallidus	Mutation(s): 2 EC: 4.2.1.84
UniProt
Find proteins for Q84FS6 (Bacillus sp. RAPc8) Explore Q84FS6 Go to UniProtKB: Q84FS6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q84FS6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
3CO (Subject of Investigation/LOI) Query on 3CO Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	COBALT (III) ION Co JAWGVVJVYSANRY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
CL (Subject of Investigation/LOI) Query on CL 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]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

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: 1.45 Å
R-Value Free: 0.184 (Depositor), 0.309 (DCC)
R-Value Work: 0.142 (Depositor), 0.290 (DCC)
R-Value Observed: 0.144 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.18	α = 90
b = 106.18	β = 90
c = 82.88	γ = 90

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-01-18

Deposition Author(s):

Funding Organization	Location	Grant Number
National Research Foundation in South Africa	South Africa	--

Revision History (Full details and data files)

Version 1.0: 2023-01-18
Type: Initial release
Version 1.1: 2024-01-31
Changes: Data collection, Refinement description
Version 1.2: 2024-11-06
Changes: 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.