2DFU

Crystal structure of the 2-hydroxyhepta-2,4-diene-1,7-dioate isomerase from Thermus Thermophilus HB8

• PDB DOI: https://doi.org/10.2210/pdb2DFU/pdb

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


• Deposited: 2006-03-03 Released: 2006-09-03 
• Deposition Author(s): Mizutani, H., Kunishima, N., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.224 
• R-Value Work: 0.197 
• R-Value Observed: 0.197 

Starting Model: experimental

Literature

Crystal structure of the 2-hydroxyhepta-2,4-diene-1,7-dioate isomerase from Thermus Thermophilus HB8

Mizutani, H., Kunishima, N.

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 (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 117.69 kDa 
• Atom Count: 8,438 
• Modelled Residue Count: 996 
• Deposited Residue Count: 1,056 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
probable 2-hydroxyhepta-2,4-diene-1,7-dioate isomerase	A, B, C, D	264	Thermus thermophilus HB8	Mutation(s): 0  EC: 5.3.3.10
UniProt
Find proteins for Q5SK43 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SK43  Go to UniProtKB:  Q5SK43

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.224 
• R-Value Work: 0.197 
• R-Value Observed: 0.197 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.34	α = 90
b = 73.412	β = 111.78
c = 122.632	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-09-03 
Deposition Author(s): Mizutani, H., Kunishima, N., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2006-09-03
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2023-10-25
  Changes: Data collection, Database references, Refinement description