9D5V

Nitrile hydratase S112D mutant

PDB DOI: https://doi.org/10.2210/pdb9D5V/pdb

Classification: LYASE
Organism(s): Pseudonocardia thermophila
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): Yes

Deposited: 2024-08-14 Released: 2024-11-06
Deposition Author(s): Miller, C.G., Liu, D., Holz, R.C.
Funding Organization(s): National Science Foundation (NSF, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.26 Å
R-Value Free: 0.230
R-Value Work: 0.212
R-Value Observed: 0.219

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Catalytic and Post-Translational Maturation Roles of a Conserved Active Site Serine Residue in Nitrile Hydratases

Miller, C.G., Knutson, K., Liu, D., Fiedler, A., Bennett, B., Holz, R.C.

To be published.

Macromolecule Content

Total Structure Weight: 49.46 kDa
Atom Count: 3,808
Modelled Residue Count: 431
Deposited Residue Count: 432
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cobalt-containing nitrile hydratase subunit alpha	A	204	Pseudonocardia thermophila	Mutation(s): 1 EC: 4.2.1.84
UniProt
Find proteins for Q7SID2 (Pseudonocardia thermophila) Explore Q7SID2 Go to UniProtKB: Q7SID2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q7SID2
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cobalt-containing nitrile hydratase subunit beta	B	228	Pseudonocardia thermophila	Mutation(s): 0 EC: 4.2.1.84
UniProt
Find proteins for Q7SID3 (Pseudonocardia thermophila) Explore Q7SID3 Go to UniProtKB: Q7SID3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q7SID3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL 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]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.26 Å
R-Value Free: 0.230
R-Value Work: 0.212
R-Value Observed: 0.219
Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.682	α = 90
b = 65.682	β = 90
c = 185.144	γ = 120

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-11-06

Deposition Author(s):

Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	CHE-2204024

Revision History (Full details and data files)

Version 1.0: 2024-11-06
Type: Initial release

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.