8I6N

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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.244 
• R-Value Work: 0.183 
• R-Value Observed: 0.186 

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.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

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

Macromolecules

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 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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CO (Subject of Investigation/LOI)	C [auth A]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSD	A	L-PEPTIDE LINKING	C3 H7 N O4 S		CYS
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 
• R-Value Work: 0.183 
• R-Value Observed: 0.186 
• 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

Entry History & Funding Information

Deposition Data

• Released Date: 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.

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

Revision History  

• Version 1.0: 2024-02-14
  Type: Initial release