3C5M | pdb_00003c5m

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.277 (Depositor), 0.290 (DCC)
R-Value Work:
0.234 (Depositor), 0.249 (DCC)
R-Value Observed:
0.234 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q87K10
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MN Query on MN Download:Ideal Coordinates CCD File SDF format, chain F [auth C] SDF format, chain E [auth B] SDF format, chain D [auth A] MOL2 format, chain F [auth C] MOL2 format, chain E [auth B] MOL2 format, chain D [auth A] mmCIF format, chain F [auth C] mmCIF format, chain E [auth B] mmCIF format, chain D [auth A]	D [auth A], E [auth B], F [auth C]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth C]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on 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 (Depositor), 0.290 (DCC)
R-Value Work: 0.234 (Depositor), 0.249 (DCC)
R-Value Observed: 0.234 (Depositor)

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

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Entry History

Deposition Data

Released Date: 2008-02-26

Deposition Author(s):

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2008-02-26
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2024-10-30
Changes: Data collection, Database references, Derived calculations, Structure summary