1WLT | pdb_00001wlt

Crystal Structure of dTDP-4-dehydrorhamnose 3,5-epimerase homologue from Sulfolobus tokodaii

• PDB DOI: https://doi.org/10.2210/pdb1WLT/pdb

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


• Deposited: 2004-06-29 Released: 2005-07-26 
• Deposition Author(s): Watanabe, N., Sakai, N., Zilian, Z., Kawarabayasi, Y., Tanaka, I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.246 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.197 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.200 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of dTDP-4-dehydrorhamnose 3,5-epimerase homologue

Watanabe, N., Sakai, N., Zilian, Z., Kawarabayasi, Y., Tanaka, I.

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)

Macromolecule Content 

• Total Structure Weight: 45.35 kDa 
• Atom Count: 3,187 
• Modeled Residue Count: 352 
• Deposited Residue Count: 392 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
176aa long hypothetical dTDP-4-dehydrorhamnose 3,5-epimerase	A, B	196	Sulfurisphaera tokodaii	Mutation(s): 0  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: 1.90 Å
• R-Value Free:  0.246 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.197 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.147	α = 90
b = 73.145	β = 90
c = 126.242	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
ADSC	data collection
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-07-26 
Deposition Author(s): Watanabe, N., Sakai, N., Zilian, Z., Kawarabayasi, Y., Tanaka, I.

Revision History  

• Version 1.0: 2005-07-26
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-10-25
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2024-10-30
  Changes: Structure summary