2ZIF

Crystal Structure of TTHA0409, Putative DNA Modification Methylase from Thermus thermophilus HB8- Complexed with S-Adenosyl-L-Methionine

PDB DOI: https://doi.org/10.2210/pdb2ZIF/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: 2.40 Å
R-Value Free: 0.273
R-Value Work: 0.217

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 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: 68.84 kDa
Atom Count: 4,047
Modelled Residue Count: 482
Deposited Residue Count: 594
Unique protein chains: 1

Macromolecules

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(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 EC: 2.1.1
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

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAM Query on SAM Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	S-ADENOSYLMETHIONINE C₁₅ H₂₂ N₆ O₅ S MEFKEPWMEQBLKI-FCKMPRQPSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
SAM	PDBBind: 2ZIF	Kd: 4.30e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.273
R-Value Work: 0.217
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.9	α = 90
b = 58.636	β = 106.06
c = 81.224	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MLPHARE	phasing

Structure Validation

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Ligand Structure Quality Assessment

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
Version 1.2: 2017-10-11
Changes: Refinement description
Version 1.3: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description