6JR8

Flavobacterium johnsoniae GH31 dextranase, FjDex31A, mutant D412A complexed with isomaltotriose

• PDB DOI: https://doi.org/10.2210/pdb6JR8/pdb

• Classification: HYDROLASE
• Organism(s): Flavobacterium johnsoniae UW101
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2019-04-02 Released: 2019-04-24 
• Deposition Author(s): Tonozuka, T.
• Funding Organization(s): Japan Society for the Promotion of Science

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.174 
• R-Value Work: 0.150 
• R-Value Observed: 0.151 

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 388.34 kDa 
• Atom Count: 30,205 
• Modelled Residue Count: 3,248 
• Deposited Residue Count: 3,352 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Candidate alpha-glycosidase Glycoside hydrolase family 31	A, B, C, D	838	Flavobacterium johnsoniae UW101	Mutation(s): 1  Gene Names: Fjoh_4430 EC: 3.2.1.20
UniProt
Find proteins for A5FBI1 (Flavobacterium johnsoniae (strain ATCC 17061 / DSM 2064 / JCM 8514 / NBRC 14942 / NCIMB 11054 / UW101)) Explore A5FBI1  Go to UniProtKB:  A5FBI1

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose	E, F, G, H	3		N/A
Glycosylation Resources
GlyTouCan:  G02998EX GlyCosmos:  G02998EX GlyGen:  G02998EX

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MPD	J [auth A], K [auth A], M [auth B], N [auth B], O [auth B], P [auth B], R [auth C], S [auth C], T [auth C], V [auth D], W [auth D], X [auth D], Y [auth D]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
ACT	I [auth A], L [auth B], Q [auth C], U [auth D]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.174 
• R-Value Work: 0.150 
• R-Value Observed: 0.151 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.37	α = 111.06
b = 112.625	β = 92.98
c = 114.172	γ = 114.54

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-04-24 
Deposition Author(s): Tonozuka, T.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science	Japan	16K07687

Revision History  

• Version 1.0: 2019-04-24
  Type: Initial release
  
• Version 1.1: 2019-10-09
  Changes: Data collection, Database references
• Version 1.2: 2020-04-01
  Changes: Data collection, Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-11-22
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary