2F7F | pdb_00002f7f

Crystal structure of Enterococcus faecalis putative nicotinate phosphoribosyltransferase, NEW YORK STRUCTURAL GENOMICS CONSORTIUM

• PDB DOI: https://doi.org/10.2210/pdb2F7F/pdb

• Classification: TRANSFERASE
• Organism(s): Enterococcus faecalis V583
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2005-11-30 Released: 2005-12-13 
• Deposition Author(s): Patskovsky, Y., Almo, S.C., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.214 (Depositor), 0.170 (DCC) 
• R-Value Work: 
  0.171 (Depositor), 0.177 (DCC) 
• R-Value Observed: 
  0.172 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Enterococcus Faecalis Nicotinate Phosphoribosyltransferase

Patskovsky, Y., Almo, S.C.

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.

Macromolecule Content 

• Total Structure Weight: 57.88 kDa 
• Atom Count: 4,404 
• Modeled Residue Count: 482 
• Deposited Residue Count: 494 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
nicotinate phosphoribosyltransferase, putative	A	494	Enterococcus faecalis V583	Mutation(s): 0  Gene Names: EF2626 EC: 2.4.2.11 (PDB Primary Data), 6.3.4.21 (UniProt)
UniProt
Find proteins for Q830Y8 (Enterococcus faecalis (strain ATCC 700802 / V583)) Explore Q830Y8  Go to UniProtKB:  Q830Y8

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DPO	L [auth A]	DIPHOSPHATE O7 P2 XPPKVPWEQAFLFU-UHFFFAOYSA-J
NIO	J [auth A], K [auth A]	NICOTINIC ACID C6 H5 N O2 PVNIIMVLHYAWGP-UHFFFAOYSA-N
SO4	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	M [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.214 (Depositor), 0.170 (DCC) 
• R-Value Work:  0.171 (Depositor), 0.177 (DCC) 
• R-Value Observed: 0.172 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.325	α = 90
b = 110.627	β = 90
c = 154.189	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-12-13 
Deposition Author(s): Patskovsky, Y., Almo, S.C., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2005-12-13
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2021-02-03
  Changes: Database references, Derived calculations, Structure summary
• Version 1.4: 2023-08-23
  Changes: Data collection, Database references, Refinement description