7BYW

Crystal structure of Acidovorax avenae L-fucose mutarotase (L-fucose-bound form)

• PDB DOI: https://doi.org/10.2210/pdb7BYW/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Paracidovorax avenae ATCC 19860
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-04-24 Released: 2020-05-27 
• Deposition Author(s): Watanabe, Y., Watanabe, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.247 
• R-Value Work: 0.226 
• R-Value Observed: 0.227 

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: homology

Macromolecule Content

• Total Structure Weight: 29.12 kDa 
• Atom Count: 2,023 
• Modelled Residue Count: 216 
• Deposited Residue Count: 240 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-fucose mutarotase	A, B	120	Paracidovorax avenae ATCC 19860	Mutation(s): 0  Gene Names: Acav_1655
UniProt
Find proteins for F0Q4R9 (Paracidovorax avenae (strain ATCC 19860 / DSM 7227 / CCUG 15838 / JCM 20985 / LMG 2117 / NCPPB 1011)) Explore F0Q4R9  Go to UniProtKB:  F0Q4R9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1PG	C [auth A], E [auth B]	2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL C11 H24 O6 SLNYBUIEAMRFSZ-UHFFFAOYSA-N
FUC (Subject of Investigation/LOI)	D [auth A], F [auth B]	alpha-L-fucopyranose C6 H12 O5 SHZGCJCMOBCMKK-SXUWKVJYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
FUC	Binding MOAD:  7BYW	Kd: 8.90e+6 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.247 
• R-Value Work: 0.226 
• R-Value Observed: 0.227 
• Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.398	α = 90
b = 68.398	β = 90
c = 69.102	γ = 120

Software Package:

Software Name	Purpose
XDS	data processing
PHENIX	refinement
PDB_EXTRACT	data extraction
Coot	model building
PHASER	phasing
Aimless	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-05-27 
Deposition Author(s): Watanabe, Y., Watanabe, S.

Revision History  

• Version 1.0: 2020-05-27
  Type: Initial release
  
• Version 1.1: 2020-06-10
  Changes: Database references
• Version 1.2: 2020-06-24
  Changes: Database references
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.4: 2023-11-29
  Changes: Data collection, Database references, Refinement description, Structure summary