2I1O

Crystal Structure of a Nicotinate Phosphoribosyltransferase from Thermoplasma acidophilum

• PDB DOI: https://doi.org/10.2210/pdb2I1O/pdb

• Classification: TRANSFERASE
• Organism(s): Thermoplasma acidophilum
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-08-14 Released: 2006-08-29 
• Deposition Author(s): Shin, D.H., Kim, R., Kim, S.-H., Berkeley Structural Genomics Center (BSGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.250 
• R-Value Work: 0.208 
• R-Value Observed: 0.208 

Literature

Crystal Structure of a zinc ion bound Nicotinate Phosphoribosyltransferase from Thermoplasma acidophilum

Shin, D.H., Kim, R., Kim, S.-H.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content

• Total Structure Weight: 44.87 kDa 
• Atom Count: 3,196 
• Modelled Residue Count: 389 
• Deposited Residue Count: 398 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nicotinate Phosphoribosyltransferase	A	398	Thermoplasma acidophilum	Mutation(s): 0  Gene Names: Ta1145
UniProt
Find proteins for Q9HJ28 (Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165)) Explore Q9HJ28  Go to UniProtKB:  Q9HJ28

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TRS	J [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
MPD	K [auth A], L [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
PO4	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
ZN	H [auth A], I [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACY	M [auth A], N [auth A]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.250 
• R-Value Work: 0.208 
• R-Value Observed: 0.208 
• Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 135.012	α = 90
b = 135.012	β = 90
c = 120.324	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
ADSC	data collection
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-08-29 
Deposition Author(s): Shin, D.H., Kim, R., Kim, S.-H., Berkeley Structural Genomics Center (BSGC)

Revision History  

• Version 1.0: 2006-08-29
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description