2ZIE

Crystal Structure of TTHA0409, Putatative DNA Modification Methylase from Thermus thermophilus HB8- Selenomethionine derivative

PDB DOI: https://doi.org/10.2210/pdb2ZIE/pdb

Classification: TRANSFERASE
Organism(s): Thermus thermophilus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-02-15 Released: 2008-07-29
Deposition Author(s): Morita, R., Ishikawa, H., Nakagawa, N., Masui, R., Yokoyama, S., Kuramitsu, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.254
R-Value Work: 0.222

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of a putative DNA methylase TTHA0409 from Thermus thermophilus HB8

Morita, R., Ishikawa, H., Nakagawa, N., Kuramitsu, S., Masui, R.

(2008) Proteins 73: 259-264

PubMed: 18618709 Search on PubMed
DOI: https://doi.org/10.1002/prot.22158
Primary Citation of Related Structures:
2ZIE, 2ZIF, 2ZIG

Organizational Affiliation

Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan.

Macromolecule Content

Total Structure Weight: 68.33 kDa
Atom Count: 3,878
Modelled Residue Count: 465
Deposited Residue Count: 594
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative modification methylase	A, B	297	Thermus thermophilus	Mutation(s): 0 Gene Names: TTHA0409
UniProt
Find proteins for Q5SL84 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SL84 Go to UniProtKB: Q5SL84
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5SL84
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.254
R-Value Work: 0.222
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.577	α = 90
b = 58.252	β = 105.52
c = 80.908	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SOLVE	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2008-07-29

Deposition Author(s):

RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History (Full details and data files)

Version 1.0: 2008-07-29
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.