7MYQ | pdb_00007myq

Crystal structure of a tRNA (guanine-N1)-methyltransferase from Acinetobacter baumannii

PDB DOI: https://doi.org/10.2210/pdb7MYQ/pdb

Classification: TRANSFERASE
Organism(s): Acinetobacter baumannii
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2021-05-21 Released: 2021-06-09
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.55 Å
R-Value Free:
0.229 (Depositor), 0.228 (DCC)
R-Value Work:
0.193 (Depositor), 0.193 (DCC)
R-Value Observed:
0.197 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of a tRNA (guanine-N1)-methyltransferase from Acinetobacter baumannii

Edwards, T.E., Abendroth, J., Horanyi, P.S., Lorimer, D.D., Seattle Structural Genomics Center for Infectious Disease (SSGCID)

To be published.

Macromolecule Content

Total Structure Weight: 57.85 kDa
Atom Count: 3,519
Modeled Residue Count: 458
Deposited Residue Count: 508
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
tRNA (guanine-N(1)-)-methyltransferase	A, B	254	Acinetobacter baumannii	Mutation(s): 0 Gene Names: trmD, ABC003_01337, ABUW_0322, EA686_14030, FDO31_01140, FJU79_00125, GNY86_14875, HYI42_11650 EC: 2.1.1.228
UniProt
Find proteins for B0V8J1 (Acinetobacter baumannii (strain AYE)) Explore B0V8J1 Go to UniProtKB: B0V8J1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B0V8J1
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.55 Å
R-Value Free: 0.229 (Depositor), 0.228 (DCC)
R-Value Work: 0.193 (Depositor), 0.193 (DCC)
R-Value Observed: 0.197 (Depositor)

Diffraction Data:

Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.25	α = 90
b = 66.25	β = 90
c = 133.01	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2021-06-09

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2021-06-09
Type: Initial release
Version 1.1: 2023-10-18
Changes: Data collection, Database references, Refinement description
Version 1.2: 2025-10-22
Changes: Database references, Structure summary

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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.