4RW0 | pdb_00004rw0

Crystal structure of a member of the lipolytic protein G-D-S-L family from Veillonella parvula DSM 2008

• PDB DOI: https://doi.org/10.2210/pdb4RW0/pdb

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


• Deposited: 2014-11-30 Released: 2015-01-28 
• Deposition Author(s): Nocek, B., Hatzos-Skintges, C., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.186 (Depositor), 0.187 (DCC) 
• R-Value Work: 
  0.157 (Depositor), 0.158 (DCC) 
• R-Value Observed: 
  0.159 (Depositor) 

Literature

Crystal structure of a member of the lipolytic protein G-D-S-L family from Veillonella parvula DSM 2008

Nocek, B., Hatzos-Skintges, C., Clancy, S., Joachimiak, A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

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

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

Macromolecule Content 

• Total Structure Weight: 42.32 kDa 
• Atom Count: 3,282 
• Modeled Residue Count: 367 
• Deposited Residue Count: 370 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lipolytic protein G-D-S-L family	A, B	185	Veillonella parvula DSM 2008	Mutation(s): 0  Gene Names: Vpar_1673

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A], E [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NA	D [auth A], F [auth B]	SODIUM ION Na FKNQFGJONOIPTF-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: 2.00 Å
• R-Value Free:  0.186 (Depositor), 0.187 (DCC) 
• R-Value Work:  0.157 (Depositor), 0.158 (DCC) 
• R-Value Observed: 0.159 (Depositor) 

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.65	α = 90
b = 121.65	β = 90
c = 84.173	γ = 120

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-01-28 
Deposition Author(s): Nocek, B., Hatzos-Skintges, C., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2015-01-28
  Type: Initial release
  
• Version 1.1: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary