2YQZ | pdb_00002yqz

Crystal Structure of Hypothetical Methyltransferase TTHA0223 from Thermus thermophilus HB8 complexed with S-adenosylmethionine

• PDB DOI: https://doi.org/10.2210/pdb2YQZ/pdb

• Classification: TRANSFERASE
• Organism(s): Thermus thermophilus HB8
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-04-01 Released: 2007-10-02 
• Deposition Author(s): Kagawa, W., Kurumizaka, H., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.235 (Depositor), 0.228 (DCC) 
• R-Value Work: 
  0.202 (Depositor), 0.195 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Literature

Crystal Structure of Hypothetical Methyltransferase TTHA0223 from Thermus thermophilus HB8 complexed with S-adenosylmethionine

Kagawa, W., Kurumizaka, H., Yokoyama, S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 60.55 kDa 
• Atom Count: 4,478 
• Modeled Residue Count: 522 
• Deposited Residue Count: 526 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein TTHA0223	A, B	263	Thermus thermophilus HB8	Mutation(s): 0  EC: 2.1.1
UniProt
Find proteins for Q5SLS0 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SLS0  Go to UniProtKB:  Q5SLS0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAM	C [auth A], D [auth B]	S-ADENOSYLMETHIONINE C15 H22 N6 O5 S MEFKEPWMEQBLKI-FCKMPRQPSA-N

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: 1.80 Å
• R-Value Free:  0.235 (Depositor), 0.228 (DCC) 
• R-Value Work:  0.202 (Depositor), 0.195 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.899	α = 87.03
b = 45.064	β = 78.96
c = 84.151	γ = 83.49

Software Package:

Software Name	Purpose
HKL-2000	data collection
RANTAN	model building
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
RANTAN	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-10-02 
Deposition Author(s): Kagawa, W., Kurumizaka, H., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2007-10-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary