6J0T | pdb_00006j0t

The crystal structure of exoinulinase INU1

• PDB DOI: https://doi.org/10.2210/pdb6J0T/pdb

• Classification: HYDROLASE
• Organism(s): Kluyveromyces marxianus DMKU3-1042
• Expression System: Komagataella pastoris
• Mutation(s): No 


• Deposited: 2018-12-26 Released: 2020-01-01 
• Deposition Author(s): Hu, X.-J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.272 (Depositor), 0.267 (DCC) 
• R-Value Work: 
  0.198 (Depositor), 0.203 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Starting Model: experimental

Literature

The Crystal Structure Study of Exoinulinase INU1

Li, L., Su, X.

To be published.

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: gel filtration

Macromolecule Content 

• Total Structure Weight: 125.56 kDa 
• Atom Count: 8,243 
• Modeled Residue Count: 1,019 
• Deposited Residue Count: 1,112 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Inulinase	A, B	556	Kluyveromyces marxianus DMKU3-1042	Mutation(s): 0  Gene Names: INU1
UniProt
Find proteins for W0T408 (Kluyveromyces marxianus (strain DMKU3-1042 / BCC 29191 / NBRC 104275)) Explore W0T408  Go to UniProtKB:  W0T408
Glycosylation
Glycosylation Sites: 1

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C, D	2		N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	E [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.272 (Depositor), 0.267 (DCC) 
• R-Value Work:  0.198 (Depositor), 0.203 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 172.65	α = 90
b = 172.65	β = 90
c = 172.65	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-01-01 
Deposition Author(s): Hu, X.-J.

Revision History  

• Version 1.0: 2020-01-01
  Type: Initial release
  
• 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, Refinement description, Structure summary
• Version 2.2: 2024-11-06
  Changes: Structure summary