2B9U | pdb_00002b9u

Crystal structure of dTDP-4-dehydrorhamnose 3,5-epimerase from sulfolobus tokodaii

• PDB DOI: https://doi.org/10.2210/pdb2B9U/pdb

• Classification: ISOMERASE
• Organism(s): Sulfurisphaera tokodaii str. 7
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2005-10-13 Released: 2006-10-13 
• Deposition Author(s): Rajakannan, V., Kondo, K., Mizushima, T., Suzuki, A., Yamane, T.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.07 Å
• R-Value Free: 
  0.257 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of dTDP-4-dehydrorhamnose 3,5-epimerase from sulfolobus tokodaii

Rajakannan, V., Kondo, K., Mizushima, T., Suzuki, A., Yamane, T.

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)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Biological Assembly 5  

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

Biological assembly 5 assigned by authors and generated by PISA (software)

Biological Assembly 6  

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

Biological assembly 6 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 246.07 kDa 
• Atom Count: 19,111 
• Modeled Residue Count: 2,112 
• Deposited Residue Count: 2,112 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
hypothetical dTDP-4-dehydrorhamnose 3,5-epimerase	A, B [auth C], C [auth D], D [auth B], E, F, G, H, I, J, K, L	176	Sulfurisphaera tokodaii str. 7	Mutation(s): 0  Gene Names: ARCHAEA EC: 5.1.3.13
UniProt
Find proteins for Q96Z62 (Sulfurisphaera tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7)) Explore Q96Z62  Go to UniProtKB:  Q96Z62

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.07 Å
• R-Value Free:  0.257 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.788	α = 90
b = 229.495	β = 96.95
c = 74.583	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-10-13 
Deposition Author(s): Rajakannan, V., Kondo, K., Mizushima, T., Suzuki, A., Yamane, T.

Revision History  

• Version 1.0: 2006-10-13
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2023-10-25
  Changes: Advisory, Data collection, Database references, Refinement description
• Version 1.4: 2024-10-30
  Changes: Structure summary