3VYH | pdb_00003vyh

Crystal structure of aW116R mutant of nitrile hydratase from Pseudonocardia thermophilla

PDB DOI: https://doi.org/10.2210/pdb3VYH/pdb

Classification: LYASE
Organism(s): Pseudonocardia thermophila
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2012-09-25 Released: 2013-11-13
Deposition Author(s): Yamanaka, Y., Sato, M., Arakawa, T., Namima, S., Hori, S., Ohtaki, A., Noguchi, K., Katayama, Y., Yohda, M., Odaka, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.63 Å
R-Value Free:
0.203 (Depositor), 0.202 (DCC)
R-Value Work:
0.174 (Depositor), 0.173 (DCC)
R-Value Observed:
0.175 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Effects of argnine residue around the substrate pocket on the substrate specificity of thiocyanate hydrolase

Yamanaka, Y., Sato, M., Arakawa, T., Namima, S., Hori, S., Ohtaki, A., Noguchi, K., Katayama, Y., Yohda, M., Odaka, M.

To be published.

Macromolecule Content

Total Structure Weight: 49.83 kDa
Atom Count: 3,818
Modeled Residue Count: 429
Deposited Residue Count: 437
Unique protein chains: 2

Macromolecules

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| 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q7SID2
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cobalt-containing nitrile hydratase subunit beta	B	233	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q7SID3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CO Query on CO 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 (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSD Query on CSD	A	L-PEPTIDE LINKING	C₃ H₇ N O₄ S		CYS
CSO Query on CSO	A	L-PEPTIDE LINKING	C₃ H₇ N O₃ S		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.63 Å
R-Value Free: 0.203 (Depositor), 0.202 (DCC)
R-Value Work: 0.174 (Depositor), 0.173 (DCC)
R-Value Observed: 0.175 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.683	α = 90
b = 65.683	β = 90
c = 184.796	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2013-11-13

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-11-13
Type: Initial release
Version 1.1: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2023-12-06
Changes: Data collection
Version 1.3: 2024-11-13
Changes: Structure summary