3EYP | pdb_00003eyp

Crystal structure of putative alpha-L-fucosidase from Bacteroides thetaiotaomicron

• PDB DOI: https://doi.org/10.2210/pdb3EYP/pdb

• Classification: structural genomics, unknown function
• Organism(s): Bacteroides thetaiotaomicron
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-10-21 Released: 2008-11-04 
• Deposition Author(s): Bonanno, J.B., Freeman, J., Bain, K.T., Hu, S., Romero, R., 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: 1.90 Å
• R-Value Free: 
  0.252 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.208 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.211 (Depositor) 

Literature

Crystal structure of putative alpha-L-fucosidase from Bacteroides thetaiotaomicron

Bonanno, J.B., Freeman, J., Bain, K.T., Hu, S., Romero, R., 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.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 107.57 kDa 
• Atom Count: 8,024 
• Modeled Residue Count: 918 
• Deposited Residue Count: 938 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative alpha-L-fucosidase	A, B	469	Bacteroides thetaiotaomicron	Mutation(s): 0  Gene Names: BT_2192 EC: 3.2.1.51
UniProt
Find proteins for Q8A5P6 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50)) Explore Q8A5P6  Go to UniProtKB:  Q8A5P6

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.252 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.208 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.211 (Depositor) 

Space Group: I 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.709	α = 90
b = 125.193	β = 90
c = 158.207	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: 2008-11-04 
Deposition Author(s): Bonanno, J.B., Freeman, J., Bain, K.T., Hu, S., Romero, R., 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: 2008-11-04
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2018-11-14
  Changes: Data collection, Structure summary
• Version 1.4: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.5: 2023-12-27
  Changes: Data collection, Database references