8I6N | pdb_00008i6n

Crystal structure of Co-type nitrile hydratase mutant from Pseudomonas thermophila - L6T

PDB DOI: https://doi.org/10.2210/pdb8I6N/pdb

Classification: LYASE
Organism(s): Pseudonocardia thermophila
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2023-01-29 Released: 2024-02-14
Deposition Author(s): Ma, D., Cheng, Z.Y., Lai, Q.P., Hou, X.D., Yin, D.J., Rao, Y.J., Zhou, Z.M.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.244 (Depositor), 0.248 (DCC)
R-Value Work:
0.183 (Depositor), 0.195 (DCC)
R-Value Observed:
0.186 (Depositor)

Starting Model: experimental
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This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of Co-type nitrile hydratase mutant L6T from Pseudomonas thermophila at 2.2 Angstroms resolution.

Cheng, Z.Y., Ma, D., Yin, M., Lai, Q.P., Peplowski, L., Han, L.C., Hou, X.D., Yin, D.J., Rao, Y.J., Zhou, Z.M.

To be published.

Macromolecule Content

Total Structure Weight: 49.92 kDa
Atom Count: 3,779
Modeled Residue Count: 427
Deposited Residue Count: 438
Unique protein chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cobalt-containing nitrile hydratase subunit alpha	A	205	Pseudonocardia thermophila	Mutation(s): 1 Gene Names: SAMN05443637_10360 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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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 (Subject of Investigation/LOI) 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: 2.20 Å
R-Value Free: 0.244 (Depositor), 0.248 (DCC)
R-Value Work: 0.183 (Depositor), 0.195 (DCC)
R-Value Observed: 0.186 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.64	α = 90
b = 65.64	β = 90
c = 184.07	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
SAINT	data scaling
SAINT	data reduction
PHENIX	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-02-14

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History (Full details and data files)

Version 1.0: 2024-02-14
Type: Initial release
Version 1.1: 2024-11-20
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.