2CU6 | pdb_00002cu6

Crystal Structure Of The dTDP-4-keto-L-rhamnose reductase-related Protein From Thermus Thermophilus HB8

• PDB DOI: https://doi.org/10.2210/pdb2CU6/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Thermus thermophilus HB8
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2005-05-25 Released: 2005-11-25 
• Deposition Author(s): Satoh, S., Yokoyama, S., Kuramitsu, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.239 (Depositor), 0.214 (DCC) 
• R-Value Work: 
  0.215 (Depositor), 0.216 (DCC) 
• R-Value Observed: 
  0.221 (Depositor) 

Literature

Crystal Structure Of The dTDP-4-keto-L-rhamnose reductase-related Protein From Thermus Thermophilus HB8

Satoh, S., Yokoyama, S., Kuramitsu, S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Dihedral - D4  (Explore in 3D)
Global Stoichiometry: Homo 8-mer - A8 

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 generated by PQS (software)

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 generated by PQS (software)

Macromolecule Content 

• Total Structure Weight: 23.08 kDa 
• Atom Count: 1,508 
• Modeled Residue Count: 182 
• Deposited Residue Count: 206 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
dTDP-4-keto-L-rhamnose reductase-related Protein	A, B	103	Thermus thermophilus HB8	Mutation(s): 2
UniProt
Find proteins for Q53W28 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q53W28  Go to UniProtKB:  Q53W28

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.239 (Depositor), 0.214 (DCC) 
• R-Value Work:  0.215 (Depositor), 0.216 (DCC) 
• R-Value Observed: 0.221 (Depositor) 

Space Group: I 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.805	α = 90
b = 121.805	β = 90
c = 121.805	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: 2005-11-25 
Deposition Author(s): Satoh, S., Yokoyama, S., Kuramitsu, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2005-11-25
  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: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary