5OPJ

Beta-L-arabinofuranosidase

• PDB DOI: https://doi.org/10.2210/pdb5OPJ/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Bacteroides thetaiotaomicron
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-08-10 Released: 2018-02-28 
• Deposition Author(s): Basle, A., Luis, A.S., Gilbert, H.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.207 
• R-Value Work: 0.168 
• R-Value Observed: 0.170 

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 92.62 kDa 
• Atom Count: 6,511 
• Modelled Residue Count: 772 
• Deposited Residue Count: 802 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Rhamnogalacturonan lyase	A	802	Bacteroides thetaiotaomicron	Mutation(s): 0  Gene Names: SAMN02910322_03495
UniProt
Find proteins for Q8AAW3 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50)) Explore Q8AAW3  Go to UniProtKB:  Q8AAW3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AHR	B [auth A]	alpha-L-arabinofuranose C5 H10 O5 HMFHBZSHGGEWLO-QMKXCQHVSA-N
ZN	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-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: 2.05 Å
• R-Value Free: 0.207 
• R-Value Work: 0.168 
• R-Value Observed: 0.170 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.21	α = 90
b = 96.21	β = 90
c = 187.84	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XDS	data scaling
Aimless	data scaling
SHELXCD	phasing
SHELXE	model building
ARP/wARP	model building
BUCCANEER	model building
Coot	model building
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-02-28 
Deposition Author(s): Basle, A., Luis, A.S., Gilbert, H.J.

Revision History  

• Version 1.0: 2018-02-28
  Type: Initial release
  
• Version 1.1: 2018-12-12
  Changes: Data collection, Database references
• Version 1.2: 2019-09-04
  Changes: Data collection, Structure summary
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary