3H7L | pdb_00003h7l

CRYSTAL STRUCTURE OF ENDOGLUCANASE-RELATED PROTEIN FROM Vibrio parahaemolyticus

• PDB DOI: https://doi.org/10.2210/pdb3H7L/pdb

• Classification: HYDROLASE
• Organism(s): Vibrio parahaemolyticus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2009-04-27 Released: 2009-05-12 
• Deposition Author(s): Patskovsky, Y., Toro, R., Morano, C., Rutter, M., Chang, S., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.232 (Depositor), 0.231 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.186 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

Literature

CRYSTAL STRUCTURE OF ENDOGLUCANASE-RELATED PROTEIN FROM Vibrio parahaemolyticus

Patskovsky, Y., Toro, R., Morano, C., Rutter, M., Chang, S., Sauder, J.M., Burley, S.K., Almo, S.C.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 200.29 kDa 
• Atom Count: 14,814 
• Modeled Residue Count: 1,726 
• Deposited Residue Count: 1,758 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ENDOGLUCANASE	A, B, C	586	Vibrio parahaemolyticus	Mutation(s): 3  Gene Names: VP2484
UniProt
Find proteins for Q87LX4 (Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633)) Explore Q87LX4  Go to UniProtKB:  Q87LX4

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	D [auth A], E [auth B], F [auth B], G [auth C], H [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.232 (Depositor), 0.231 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.186 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 166.124	α = 90
b = 166.124	β = 90
c = 343.534	γ = 120

Software Package:

Software Name	Purpose
SHELXD	phasing
REFMAC	refinement
DENZO	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-05-12 
Deposition Author(s): Patskovsky, Y., Toro, R., Morano, C., Rutter, M., Chang, S., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2009-05-12
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2018-11-21
  Changes: Data collection, Structure summary
• Version 1.3: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.4: 2021-10-13
  Changes: Database references
• Version 1.5: 2024-02-21
  Changes: Data collection