3TOV | pdb_00003tov

The crystal structure of the glycosyl transferase family 9 from Veillonella parvula DSM 2008

• PDB DOI: https://doi.org/10.2210/pdb3TOV/pdb

• Classification: TRANSFERASE
• Organism(s): Veillonella parvula DSM 2008
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-09-06 Released: 2011-09-21 
• Deposition Author(s): Tan, K., Marshall, N., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.98 Å
• R-Value Free: 
  0.267 (Depositor), 0.259 (DCC) 
• R-Value Work: 
  0.171 (Depositor), 0.172 (DCC) 
• R-Value Observed: 
  0.176 (Depositor) 

Literature

The crystal structure of the glycosyl transferase family 9 from Veillonella parvula DSM 2008

Tan, K., Marshall, N., Clancy, S., Joachimiak, A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 80.89 kDa 
• Atom Count: 5,539 
• Modeled Residue Count: 692 
• Deposited Residue Count: 698 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycosyl transferase family 9	A, B	349	Veillonella parvula DSM 2008	Mutation(s): 0  Gene Names: Vpar_0760

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth B], I [auth B], J [auth B], K [auth B], L [auth B], M [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

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: 2.98 Å
• R-Value Free:  0.267 (Depositor), 0.259 (DCC) 
• R-Value Work:  0.171 (Depositor), 0.172 (DCC) 
• R-Value Observed: 0.176 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.708	α = 90
b = 95.394	β = 90
c = 121.494	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
SHELXD	phasing
MLPHARE	phasing
DM	model building
RESOLVE	model building
HKL-3000	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-09-21 
Deposition Author(s): Tan, K., Marshall, N., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2011-09-21
  Type: Initial release
  
• Version 1.1: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary