5X7F | pdb_00005x7f

Structure of a O-methyltransferase from Mycobacterium tuberculosis at 2.0 resolution

PDB DOI: https://doi.org/10.2210/pdb5X7F/pdb

Classification: TRANSFERASE
Organism(s): Mycobacterium tuberculosis H37Rv
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2017-02-25 Released: 2017-03-29
Deposition Author(s): Yan, Q., Jiang, D.
Funding Organization(s): National Basic Research Program of China

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.216 (Depositor), 0.220 (DCC)
R-Value Work:
0.192 (Depositor), 0.190 (DCC)
R-Value Observed:
0.193 (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

Structure of a O-methyltransferase from Mycobacterium tuberculosis at 2.0 resolution

Yan, Q., Jiang, D.

To be published.

Macromolecule Content

Total Structure Weight: 24.7 kDa
Atom Count: 1,555
Modeled Residue Count: 198
Deposited Residue Count: 235
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative O-methyltransferase Rv1220c	A	235	Mycobacterium tuberculosis H37Rv	Mutation(s): 0 Gene Names: Rv1220c EC: 2.1.1
UniProt
Find proteins for P9WJZ7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WJZ7 Go to UniProtKB: P9WJZ7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P9WJZ7
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.216 (Depositor), 0.220 (DCC)
R-Value Work: 0.192 (Depositor), 0.190 (DCC)
R-Value Observed: 0.193 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.7	α = 90
b = 57.7	β = 90
c = 158.163	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2017-03-29

Deposition Author(s):

Funding Organization	Location	Grant Number
National Basic Research Program of China	China	2013EB091991

Revision History (Full details and data files)

Version 1.0: 2017-03-29
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, 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.