1WX1 | pdb_00001wx1

Crystal structure of nictinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase from Thermus thermophilus HB8

• PDB DOI: https://doi.org/10.2210/pdb1WX1/pdb

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


• Deposited: 2005-01-19 Released: 2005-02-01 
• Deposition Author(s): Asada, Y., Kunishima, N., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.97 Å
• R-Value Free: 
  0.219 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.184 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

Literature

Crystal structure of nictinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase from Thermus thermophilus HB8

Asada, Y., 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)

Macromolecule Content 

• Total Structure Weight: 69.6 kDa 
• Atom Count: 5,270 
• Modeled Residue Count: 660 
• Deposited Residue Count: 670 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase	A, B	335	Thermus thermophilus HB8	Mutation(s): 0  EC: 2.4.2.21
UniProt
Find proteins for Q7SIC7 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q7SIC7  Go to UniProtKB:  Q7SIC7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NA	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.97 Å
• R-Value Free:  0.219 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.184 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.357	α = 90
b = 107.357	β = 90
c = 244.665	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-02-01 
Deposition Author(s): Asada, Y., Kunishima, N., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2005-02-01
  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: 2011-11-16
  Changes: Atomic model
• Version 1.4: 2024-03-13
  Changes: Data collection, Database references, Derived calculations