2ZIE | pdb_00002zie

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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.254 (Depositor), 0.251 (DCC) 
• R-Value Work: 
  0.222 (Depositor), 0.215 (DCC) 

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

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

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

Macromolecules

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

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
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 (Depositor), 0.251 (DCC) 
• R-Value Work:  0.222 (Depositor), 0.215 (DCC) 

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

Entry History 

Deposition Data

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

Revision History  

• Version 1.0: 2008-07-29
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Structure summary