4EVW

Crystal Structure of the nucleoside-diphosphate-sugar pyrophosphorylase from Vibrio cholerae RC9. Northeast Structural Genomics Consortium (NESG) Target VcR193.

• PDB DOI: https://doi.org/10.2210/pdb4EVW/pdb

• Classification: TRANSFERASE
• Organism(s): Vibrio cholerae RC9
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2012-04-26 Released: 2012-05-23 
• Deposition Author(s): Vorobiev, S., Neely, H., Su, M., Seetharaman, J., Mao, M., Xiao, R., Kohan, E., Everett, J.K., Acton, T.B., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.203 
• R-Value Work: 0.184 
• R-Value Observed: 0.185 

Literature

Crystal Structure of the nucleoside-diphosphate-sugar pyrophosphorylase from Vibrio cholerae RC9.

Vorobiev, S., Neely, H., Su, M., Seetharaman, J., Mao, M., Xiao, R., Kohan, E., Everett, J.K., Acton, T.B., Montelione, G.T., Tong, L., Hunt, J.F.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 59.21 kDa 
• Atom Count: 4,383 
• Modelled Residue Count: 488 
• Deposited Residue Count: 510 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleoside-diphosphate-sugar pyrophosphorylase	A, B	255	Vibrio cholerae RC9	Mutation(s): 1  Gene Names: VCC_000301

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	C [auth A], D [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.203 
• R-Value Work: 0.184 
• R-Value Observed: 0.185 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.303	α = 90
b = 117.003	β = 90
c = 128.561	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SnB	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-05-23 
Deposition Author(s): Vorobiev, S., Neely, H., Su, M., Seetharaman, J., Mao, M., Xiao, R., Kohan, E., Everett, J.K., Acton, T.B., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

Revision History  

• Version 1.0: 2012-05-23
  Type: Initial release
  
• Version 1.1: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary