2YUT | pdb_00002yut

Crystal Structure of Putative Short-Chain Oxidoreductase TTHB094 from Thermus thermophilus HB8

• PDB DOI: https://doi.org/10.2210/pdb2YUT/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Thermus thermophilus HB8
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2007-04-06 Released: 2007-10-09 
• Deposition Author(s): Agari, Y., Shinkai, A., Yokoyama, S., Kuramitsu, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.224 (Depositor), 0.214 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.181 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

Literature

Crystal Structure of Putative Short-Chain Oxidoreductase TTHB094 from Thermus thermophilus HB8

Agari, Y., Shinkai, A., Kuramitsu, S.

To be published.

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,PQS (software)

Macromolecule Content 

• Total Structure Weight: 22.53 kDa 
• Atom Count: 1,656 
• Modeled Residue Count: 202 
• Deposited Residue Count: 207 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative short-chain oxidoreductase	A	207	Thermus thermophilus HB8	Mutation(s): 2
UniProt
Find proteins for Q53W68 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q53W68  Go to UniProtKB:  Q53W68

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP	B [auth A]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.224 (Depositor), 0.214 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.181 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 149.091	α = 90
b = 149.091	β = 90
c = 47.721	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
BSS	data collection
CrystalClear	data reduction
CrystalClear	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-10-09 
Deposition Author(s): Agari, Y., Shinkai, A., Yokoyama, S., Kuramitsu, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2007-10-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Derived calculations, Source and taxonomy, Version format compliance
• Version 1.2: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Structure summary