6W14 | pdb_00006w14

Crystal structure of tRNA (guanine-N(1)-)-methyltransferase from Mycobacterium smegmatis

PDB DOI: https://doi.org/10.2210/pdb6W14/pdb

Classification: TRANSFERASE
Organism(s): Mycolicibacterium smegmatis MC2 155
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-03-03 Released: 2020-05-06
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.279 (Depositor), 0.281 (DCC)
R-Value Work:
0.211 (Depositor), 0.213 (DCC)
R-Value Observed:
0.218 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 6W14

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of tRNA (guanine-N(1)-)-methyltransferase from Mycobacterium smegmatis

Dranow, D.M., Bolejack, M.J., Abendroth, J.A., Lorimer, D.D., Horanyi, P.S., Edwards, T.E.

To be published.

Macromolecule Content

Total Structure Weight: 26.06 kDa
Atom Count: 1,603
Modeled Residue Count: 203
Deposited Residue Count: 234
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
tRNA (guanine-N(1)-)-methyltransferase	A	234	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0 Gene Names: trmD, MSMEI_2377 EC: 2.1.1.228
UniProt
Find proteins for A0QV40 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0QV40 Go to UniProtKB: A0QV40
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0QV40
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.279 (Depositor), 0.281 (DCC)
R-Value Work: 0.211 (Depositor), 0.213 (DCC)
R-Value Observed: 0.218 (Depositor)

Diffraction Data:

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.46	α = 90
b = 58.46	β = 90
c = 114.44	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MoRDa	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2020-05-06

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2020-05-06
Type: Initial release
Version 1.1: 2023-10-18
Changes: Data collection, Database references, Refinement description
Version 1.2: 2025-10-22
Changes: Structure summary

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.