6B5F

Crystal structure of nicotinate mononucleotide-5,6-dimethylbenzimidazole phosphoribosyltransferase CobT from Yersinia enterocolitica

• PDB DOI: https://doi.org/10.2210/pdb6B5F/pdb

• Classification: TRANSFERASE
• Organism(s): Yersinia enterocolitica subsp. enterocolitica 8081
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-09-29 Released: 2017-10-18 
• Deposition Author(s): Stogios, P.J., Skarina, T., McChesney, C., Grimshaw, T., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.180 
• R-Value Work: 0.150 
• R-Value Observed: 0.151 

Starting Model: experimental

Literature

Crystal structure of nicotinate mononucleotide-5,6-dimethylbenzimidazole phosphoribosyltransferase CobT from Yersinia enterocolitica

Stogios, P.J.

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: 73.57 kDa 
• Atom Count: 5,832 
• Modelled Residue Count: 680 
• Deposited Residue Count: 708 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase	A, B	354	Yersinia enterocolitica subsp. enterocolitica 8081	Mutation(s): 0  Gene Names: cobT, YE2707 EC: 2.4.2.21
UniProt
Find proteins for A1JTP8 (Yersinia enterocolitica serotype O:8 / biotype 1B (strain NCTC 13174 / 8081)) Explore A1JTP8  Go to UniProtKB:  A1JTP8

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], E [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	F [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.180 
• R-Value Work: 0.150 
• R-Value Observed: 0.151 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.155	α = 90
b = 73.875	β = 90
c = 119	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing
PHENIX	model building
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-10-18 
Deposition Author(s): Stogios, P.J., Skarina, T., McChesney, C., Grimshaw, T., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201200026C

Revision History  

• Version 1.0: 2017-10-18
  Type: Initial release
  
• Version 1.1: 2019-12-11
  Changes: Author supporting evidence
• Version 1.2: 2023-10-04
  Changes: Data collection, Database references, Refinement description