7CVV | pdb_00007cvv

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

PDB DOI: https://doi.org/10.2210/pdb7CVV/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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.52 Å
R-Value Free:
0.217 (Depositor), 0.220 (DCC)
R-Value Work:
0.178 (Depositor), 0.190 (DCC)
R-Value Observed:
0.180 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Structural and Biochemical analysis of FumaraseC from Mannheimia succiniciproducens

Kim, B., Lee, S.H., Kim, K.J.

To be published.

Macromolecule Content

Total Structure Weight: 76.58 kDa
Atom Count: 5,110
Modeled Residue Count: 657
Deposited Residue Count: 687
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
O-methyltransferase family 3	A, B, C	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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	G8T6H8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAM (Subject of Investigation/LOI) Query on SAM Download Ideal Coordinates CCD File SDF format, chain F [auth C] SDF format, chain E [auth B] SDF format, chain D [auth A] MOL2 format, chain F [auth C] MOL2 format, chain E [auth B] MOL2 format, chain D [auth A] mmCIF format, chain F [auth C] mmCIF format, chain E [auth B] mmCIF format, chain D [auth A]	D [auth A], E [auth B], F [auth C]	S-ADENOSYLMETHIONINE C₁₅ H₂₂ N₆ O₅ S MEFKEPWMEQBLKI-FCKMPRQPSA-N		Interactions Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.52 Å
R-Value Free: 0.217 (Depositor), 0.220 (DCC)
R-Value Work: 0.178 (Depositor), 0.190 (DCC)
R-Value Observed: 0.180 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 166.185	α = 90
b = 93.181	β = 104.12
c = 43.335	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2021-09-01

Deposition Author(s):

Revision History (Full details and data files)

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

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.