1OY5

Crystal structure of tRNA (m1G37) methyltransferase from Aquifex aeolicus

PDB DOI: https://doi.org/10.2210/pdb1OY5/pdb

Classification: TRANSFERASE
Organism(s): Aquifex aeolicus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2003-04-03 Released: 2003-11-11
Deposition Author(s): Liu, J., Wang, W., Shin, D.H., Yokota, H., Kim, R., Kim, S.H., Berkeley Structural Genomics Center (BSGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.300 (Depositor), 0.300 (DCC)
R-Value Work:
0.279 (Depositor), 0.280 (DCC)
R-Value Observed:
0.280 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of tRNA (m1G37) methyltransferase from Aquifex aeolicus at 2.6 A resolution: a novel methyltransferase fold.

Liu, J., Wang, W., Shin, D.H., Yokota, H., Kim, R., Kim, S.H.

(2003) Proteins 53: 326-328

PubMed: 14517984 Search on PubMed
DOI: https://doi.org/10.1002/prot.10479
Primary Citation of Related Structures:
1OY5

Organizational Affiliation

Department of Chemistry, University of California, Berkeley, California, USA.

Macromolecule Content

Total Structure Weight: 89.08 kDa
Atom Count: 5,379
Modelled Residue Count: 654
Deposited Residue Count: 771
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
tRNA (Guanine-N(1)-)-methyltransferase	A, B, C	257	Aquifex aeolicus	Mutation(s): 0 Gene Names: TRMD OR AQ_1489 EC: 2.1.1.31 (PDB Primary Data), 2.1.1.228 (UniProt)
UniProt
Find proteins for O67463 (Aquifex aeolicus (strain VF5)) Explore O67463 Go to UniProtKB: O67463
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O67463
Sequence Annotations Expand
Reference Sequence LOADING

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.300 (Depositor), 0.300 (DCC)
R-Value Work: 0.279 (Depositor), 0.280 (DCC)
R-Value Observed: 0.280 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 153.351	α = 90
b = 96.139	β = 96.24
c = 57.426	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
HKL-2000	data reduction
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2003-11-11

Deposition Author(s):

Berkeley Structural Genomics Center (BSGC)

Revision History (Full details and data files)

Version 1.0: 2003-11-11
Type: Initial release
Version 1.1: 2008-04-29
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.3: 2024-10-30
Changes: Data collection, Database references, Structure summary

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.