1X1E | pdb_00001x1e

Crystal Structure of TT0495 protein from Thermus thermophilus HB8

• PDB DOI: https://doi.org/10.2210/pdb1X1E/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Thermus thermophilus HB8
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2005-04-04 Released: 2006-07-11 
• Deposition Author(s): Lokanath, N.K., Terao, Y., Kunishima, N., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 
  0.215 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.203 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of TT0495 protein from Thermus thermophilus HB8

Lokanath, N.K., Terao, Y., Kunishima, N.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 25.7 kDa 
• Atom Count: 1,993 
• Modeled Residue Count: 239 
• Deposited Residue Count: 239 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-deoxy-D-gluconate 3-dehydrogenase	A	239	Thermus thermophilus HB8	Mutation(s): 0  EC: 1.1.1.125
UniProt
Find proteins for Q53W82 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q53W82  Go to UniProtKB:  Q53W82

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free:  0.215 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.203 (Depositor) 

Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.712	α = 90
b = 62.712	β = 90
c = 111.272	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-07-11 
Deposition Author(s): Lokanath, N.K., Terao, Y., Kunishima, N., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2006-07-11
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Source and taxonomy, Version format compliance
• Version 1.3: 2023-10-25
  Changes: Data collection, Database references, Refinement description