3C5M

Crystal structure of oligogalacturonate lyase (VPA0088) from Vibrio parahaemolyticus. Northeast Structural Genomics Consortium Target VpR199

• PDB DOI: https://doi.org/10.2210/pdb3C5M/pdb

• Classification: LYASE
• Organism(s): Vibrio parahaemolyticus RIMD 2210633
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-01-31 Released: 2008-02-26 
• Deposition Author(s): Forouhar, F., Abashidze, M., Seetharaman, J., Janjua, H., Mao, L., Xiao, R., Owens, L.A., Wang, D., Baran, M.C., Acton, T.B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.277 
• R-Value Work: 0.234 
• R-Value Observed: 0.234 

Literature

Crystal structure of oligogalacturonate lyase (VPA0088) from Vibrio parahaemolyticus.

Forouhar, F., Abashidze, M., Seetharaman, J., Janjua, H., Mao, L., Xiao, R., Owens, L.A., Wang, D., Baran, M.C., Acton, T.B., Montelione, G.T., Hunt, J.F., Tong, L.

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)

Biological Assembly 3  

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

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

Macromolecule Content

• Total Structure Weight: 137.23 kDa 
• Atom Count: 9,292 
• Modelled Residue Count: 1,130 
• Deposited Residue Count: 1,188 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Oligogalacturonate lyase	A, B, C	396	Vibrio parahaemolyticus RIMD 2210633	Mutation(s): 0  Gene Names: VPA0088
UniProt
Find proteins for Q87K10 (Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633)) Explore Q87K10  Go to UniProtKB:  Q87K10

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MN	D [auth A], E [auth B], F [auth C]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.277 
• R-Value Work: 0.234 
• R-Value Observed: 0.234 
• Space Group: P 3 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.233	α = 90
b = 115.233	β = 90
c = 209.95	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
ADSC	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
SHELXD	phasing
SOLVE	phasing
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-02-26 
Deposition Author(s): Forouhar, F., Abashidze, M., Seetharaman, J., Janjua, H., Mao, L., Xiao, R., Owens, L.A., Wang, D., Baran, M.C., Acton, T.B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

Revision History  

• Version 1.0: 2008-02-26
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance