7CVW | pdb_00007cvw

Crystal structure of Catechol o-methyl transferase (COMT) from Niastella koreensis

• PDB DOI: https://doi.org/10.2210/pdb7CVW/pdb

• Classification: TRANSFERASE
• Organism(s): Niastella koreensis GR20-10
• Expression System: Escherichia coli K-12
• Mutation(s): No 


• Deposited: 2020-08-27 Released: 2021-09-01 
• Deposition Author(s): Kim, B., Lee, S.H., Kim, K.-J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.54 Å
• R-Value Free: 
  0.195 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.174 (Depositor) 
• R-Value Observed: 
  0.175 (Depositor) 

Starting Model: experimental

Literature

Structural and Biochemical analysis of FumaraseC from Mannheimia succiniciproducens

Kim, B., Lee, S.H., Kim, K.J.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 51.26 kDa 
• Atom Count: 3,569 
• Modeled Residue Count: 438 
• Deposited Residue Count: 458 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
O-methyltransferase family 3	A, B	229	Niastella koreensis GR20-10	Mutation(s): 0  Gene Names: Niako_0425 EC: 2.1.1.6
UniProt
Find proteins for G8T6H8 (Niastella koreensis (strain DSM 17620 / KACC 11465 / NBRC 106392 / GR20-10)) Explore G8T6H8  Go to UniProtKB:  G8T6H8

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAH (Subject of Investigation/LOI)	E [auth A], H [auth B]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N
GOL	D [auth A], G [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)	C [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.54 Å
• R-Value Free:  0.195 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.174 (Depositor) 
• R-Value Observed: 0.175 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.689	α = 90
b = 98.226	β = 90
c = 101.773	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-09-01 
Deposition Author(s): Kim, B., Lee, S.H., Kim, K.-J.

Revision History  

• Version 1.0: 2021-09-01
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description