2YVW

Crystal structure of UDP-N-acetylglucosamine 1-carboxyvinyltransferase from Aquifex aeolicus VF5

• PDB DOI: https://doi.org/10.2210/pdb2YVW/pdb

• Classification: TRANSFERASE
• Organism(s): Aquifex aeolicus VF5
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-04-16 Released: 2007-10-16 
• Deposition Author(s): Kitamuta, Y., Yokoyama, S., Kuramitsu, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.81 Å
• R-Value Free: 0.220 
• R-Value Work: 0.195 
• R-Value Observed: 0.195 

Starting Model: experimental

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 3SWG

Literature

Crystal structure of UDP-N-acetylglucosamine 1-carboxyvinyltransferase from Aquifex aeolicus VF5

Kitamura, Y., Yokoyama, S., Kuramitsu, S.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 48.09 kDa 
• Atom Count: 3,585 
• Modelled Residue Count: 416 
• Deposited Residue Count: 425 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-N-acetylglucosamine 1-carboxyvinyltransferase	A	425	Aquifex aeolicus VF5	Mutation(s): 0  EC: 2.5.1.7
UniProt
Find proteins for O67315 (Aquifex aeolicus (strain VF5)) Explore O67315  Go to UniProtKB:  O67315

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EPU	C [auth A]	URIDINE-DIPHOSPHATE-2(N-ACETYLGLUCOSAMINYL) BUTYRIC ACID C20 H29 N3 O19 P2 BEGZZYPUNCJHKP-DBYWSUQTSA-N
PO4	B [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.81 Å
• R-Value Free: 0.220 
• R-Value Work: 0.195 
• R-Value Observed: 0.195 
• Space Group: P 6₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 132.004	α = 90
b = 132.004	β = 90
c = 58.165	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-10-16 
Deposition Author(s): Kitamuta, Y., Yokoyama, S., Kuramitsu, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2007-10-16
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description