3KY7 | pdb_00003ky7

2.35 Angstrom resolution crystal structure of a putative tRNA (guanine-7-)-methyltransferase (trmD) from Staphylococcus aureus subsp. aureus MRSA252

PDB DOI: https://doi.org/10.2210/pdb3KY7/pdb

Classification: TRANSFERASE
Organism(s): Staphylococcus aureus subsp. aureus MRSA252
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-12-04 Released: 2009-12-22
Deposition Author(s): Halavaty, A.S., Minasov, G., Winsor, J., Dubrovska, I., Shuvalova, L., See, R., Zoraghi, R., Reiner, N., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free:
0.255 (Depositor), 0.267 (DCC)
R-Value Work:
0.209 (Depositor), 0.226 (DCC)
R-Value Observed:
0.211 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3KY7

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

Literature

2.35 Angstrom resolution crystal structure of a putative tRNA (guanine-7-)-methyltransferase (trmD) from Staphylococcus aureus subsp. aureus MRSA252

Halavaty, A.S., Minasov, G., Winsor, J., Dubrovska, I., Shuvalova, L., See, R., Zoraghi, R., Reiner, N., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 30.85 kDa
Atom Count: 1,945
Modeled Residue Count: 229
Deposited Residue Count: 269
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	269	Staphylococcus aureus subsp. aureus MRSA252	Mutation(s): 0 Gene Names: SAR1216, trmD EC: 2.1.1.31 (PDB Primary Data), 2.1.1.228 (UniProt)
UniProt
Find proteins for Q6GHJ5 (Staphylococcus aureus (strain MRSA252)) Explore Q6GHJ5 Go to UniProtKB: Q6GHJ5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6GHJ5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
OCS Query on OCS	A	L-PEPTIDE LINKING	C₃ H₇ N O₅ S		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free: 0.255 (Depositor), 0.267 (DCC)
R-Value Work: 0.209 (Depositor), 0.226 (DCC)
R-Value Observed: 0.211 (Depositor)

Diffraction Data:

Space Group: P 4₃ 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 125.176	α = 90
b = 125.176	β = 90
c = 125.176	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
HKL-3000	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2009-12-22

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2009-12-22
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2017-11-01
Changes: Refinement description
Version 1.3: 2025-03-26
Changes: Data collection, Database references, Derived calculations, 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.