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), 0.193 (DCC)
R-Value Observed:
0.193 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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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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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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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), 0.193 (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

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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

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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.