4ZRX | pdb_00004zrx

Crystal structure of a putative alpha-L-fucosidase (BACOVA_04357) from Bacteroides ovatus ATCC 8483 at 1.59 A resolution

• PDB DOI: https://doi.org/10.2210/pdb4ZRX/pdb

• Classification: HYDROLASE
• Organism(s): Bacteroides ovatus ATCC 8483
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-05-12 Released: 2015-05-27 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.59 Å
• R-Value Free: 
  0.175 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.151 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.153 (Depositor) 

Literature

Crystal structure of a putative alpha-L-fucosidase (BACOVA_04357) from Bacteroides ovatus ATCC 8483 at 1.59 A resolution

Joint Center for Structural Genomics (JCSG)

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: 67.81 kDa 
• Atom Count: 5,399 
• Modeled Residue Count: 581 
• Deposited Residue Count: 586 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
F5/8 type C domain protein	A	586	Bacteroides ovatus ATCC 8483	Mutation(s): 0  Gene Names: BACOVA_04357

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.59 Å
• R-Value Free:  0.175 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.151 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.153 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M3JC7B

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.021	α = 90
b = 71.754	β = 106.98
c = 73.106	γ = 90

Software Package:

Software Name	Purpose
PDB_EXTRACT	data extraction
SHELX	phasing
SHARP	phasing
XSCALE	data scaling
REFMAC	refinement
SHELXD	phasing
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-05-27 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2015-05-27
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Derived calculations, Refinement description, Source and taxonomy
• Version 1.2: 2018-01-24
  Changes: Database references
• Version 1.3: 2023-02-01
  Changes: Data collection, Database references
• Version 1.4: 2024-10-23
  Changes: Data collection, Structure summary