3GM8

Crystal structure of a beta-glycosidase from Bacteroides vulgatus

• PDB DOI: https://doi.org/10.2210/pdb3GM8/pdb

• Classification: HYDROLASE
• Organism(s): Phocaeicola vulgatus ATCC 8482
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-03-13 Released: 2009-03-31 
• Deposition Author(s): Bonanno, J.B., Rutter, M., Bain, K.T., Iizuka, M., Ozyurt, S., Wasserman, 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: 2.40 Å
• R-Value Free: 0.287 
• R-Value Work: 0.226 
• R-Value Observed: 0.229 

Literature

Crystal structure of a beta-glycosidase from Bacteroides vulgatus

Bonanno, J.B., Rutter, M., Bain, K.T., Iizuka, M., Ozyurt, S., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C.

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)

Macromolecule Content

• Total Structure Weight: 91.27 kDa 
• Atom Count: 6,380 
• Modelled Residue Count: 770 
• Deposited Residue Count: 801 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycoside hydrolase family 2, candidate beta-glycosidase	A	801	Phocaeicola vulgatus ATCC 8482	Mutation(s): 0  Gene Names: BVU_0391 EC: 3.2.1
UniProt
Find proteins for A6KXE5 (Phocaeicola vulgatus (strain ATCC 8482 / DSM 1447 / JCM 5826 / CCUG 4940 / NBRC 14291 / NCTC 11154)) Explore A6KXE5  Go to UniProtKB:  A6KXE5

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.287 
• R-Value Work: 0.226 
• R-Value Observed: 0.229 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.754	α = 90
b = 193.348	β = 90
c = 190.667	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
SHELXCD	phasing
SHELXE	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-03-31 
Deposition Author(s): Bonanno, J.B., Rutter, M., Bain, K.T., Iizuka, M., Ozyurt, S., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2009-03-31
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2018-11-21
  Changes: Data collection, Structure summary
• Version 1.4: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.5: 2024-02-21
  Changes: Data collection, Database references