3L0G | pdb_00003l0g

Crystal structure of Nicotinate-nucleotide pyrophosphorylase from Ehrlichia chaffeensis at 2.05A resolution

• PDB DOI: https://doi.org/10.2210/pdb3L0G/pdb

• Classification: TRANSFERASE
• Organism(s): Ehrlichia chaffeensis str. Arkansas
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-12-09 Released: 2009-12-22 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 
  0.226 (Depositor), 0.225 (DCC) 
• R-Value Work: 
  0.174 (Depositor), 0.175 (DCC) 
• R-Value Observed: 
  0.177 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Nicotinate-nucleotide pyrophosphorylase from Ehrlichia chaffeensis at 2.05A resolution

Seattle Structural Genomics Center for Infectious Disease (SSGCID), Abendroth, J., Sankaran, B., Arakaki, T., Staker, B.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 133.36 kDa 
• Atom Count: 9,292 
• Modeled Residue Count: 1,093 
• Deposited Residue Count: 1,200 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nicotinate-nucleotide pyrophosphorylase	A, B, C, D	300	Ehrlichia chaffeensis str. Arkansas	Mutation(s): 0  Gene Names: nadC, ECH_0026 EC: 2.4.2.19
UniProt
Find proteins for Q2GI74 (Ehrlichia chaffeensis (strain ATCC CRL-10679 / Arkansas)) Explore Q2GI74  Go to UniProtKB:  Q2GI74

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	E [auth A], G [auth B], I [auth C], K [auth D]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
FMT	F [auth A], H [auth B], J [auth C], L [auth D]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free:  0.226 (Depositor), 0.225 (DCC) 
• R-Value Work:  0.174 (Depositor), 0.175 (DCC) 
• R-Value Observed: 0.177 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33L0G

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.53	α = 113.01
b = 77.32	β = 91.82
c = 78.32	γ = 111.68

Software Package:

Software Name	Purpose
BOS	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-12-22 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2009-12-22
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance
• Version 1.2: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-11-20
  Changes: Structure summary