5HDR | pdb_00005hdr

Crystal structure of a bacterial fucosidase with iminocyclitol (2S,3S,4R,5S)-3,4-dihydroxy-2-ethynyl-5-methylpyrrolidine

• PDB DOI: https://doi.org/10.2210/pdb5HDR/pdb

• Classification: HYDROLASE
• Organism(s): Bacteroides thetaiotaomicron VPI-5482
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-01-05 Released: 2016-02-03 
• Deposition Author(s): Wright, D.W., Davies, G.J.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.243 (Depositor), 0.247 (DCC) 
• R-Value Work: 
  0.201 (Depositor), 0.206 (DCC) 
• R-Value Observed: 
  0.203 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a bacterial fucosidase with iminocyclitol (2S,3S,4R,5S)-3,4-dihydroxy-2-ethynyl-5-methylpyrrolidine

Wright, D.W., Davies, G.J.

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.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 209.36 kDa 
• Atom Count: 14,754 
• Modeled Residue Count: 1,761 
• Deposited Residue Count: 1,788 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-L-fucosidase	A, B, C, D	447	Bacteroides thetaiotaomicron VPI-5482	Mutation(s): 0  Gene Names: BT_2970 EC: 3.2.1.51
UniProt
Find proteins for Q8A3I4 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50)) Explore Q8A3I4  Go to UniProtKB:  Q8A3I4

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
H79	H [auth A], L [auth B], O [auth C], Q [auth D]	[(1,2,3,4,5-eta)-cyclopentadienyl][(1,2,3,4,5-eta)-1-{3-[4-(3,4-dihydroxy-5-methylpyrrolidin-2-yl)-1H-1,2,3-triazol-1-yl]prop-1-en-1-yl}cyclopentadienyl]iron C20 H15 Fe N4 O2 FQODPMWJAJVXMD-YCHRPOLYSA-N
SO4	E [auth A], F [auth A], I [auth B], J [auth B], M [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
IMD	G [auth A], K [auth B], N [auth C], P [auth D]	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.243 (Depositor), 0.247 (DCC) 
• R-Value Work:  0.201 (Depositor), 0.206 (DCC) 
• R-Value Observed: 0.203 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.5	α = 90
b = 188.76	β = 93.89
c = 98.14	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
Aimless	data scaling

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-02-03 
Deposition Author(s): Wright, D.W., Davies, G.J.

---

Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council	United Kingdom	--

Revision History  

• Version 1.0: 2016-02-03
  Type: Initial release
  
• Version 1.1: 2017-08-30
  Changes: Author supporting evidence
• Version 1.2: 2024-01-10
  Changes: Data collection, Database references, Refinement description