2ZIF

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.217 

wwPDB Validation 3D Report Full Report


This is version 1.2 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


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Putative modification methylase
A, B
297Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
EC: 2.1.1.-
Find proteins for Q5SL84 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SL84
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SAM
Query on SAM

Download SDF File 
Download CCD File 
A, B
S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
SAMKd: 43000 nM BINDINGMOAD
SAMKd: 43000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.217 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 63.900α = 90.00
b = 58.636β = 106.06
c = 81.224γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
HKL-2000data collection
DENZOdata reduction
CNSrefinement
HKL-2000data scaling
HKL-2000data reduction
MLPHAREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-07-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-10-11
    Type: Refinement description