4J3S

Crystal structure of barley limit dextrinase soaked with 300mM maltotetraose

• PDB DOI: https://doi.org/10.2210/pdb4J3S/pdb

• Classification: HYDROLASE
• Organism(s): Hordeum vulgare
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-02-06 Released: 2014-02-12 
• Deposition Author(s): Sim, L., Windahl, M.S., Moeller, M.S., Henriksen, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.182 
• R-Value Work: 0.136 
• R-Value Observed: 0.138 

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 102.48 kDa 
• Atom Count: 7,349 
• Modelled Residue Count: 854 
• Deposited Residue Count: 905 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Limit dextrinase	A	905	Hordeum vulgare	Mutation(s): 0  EC: 3.2.1.41
UniProt
Find proteins for Q9FYY0 (Hordeum vulgare) Explore Q9FYY0  Go to UniProtKB:  Q9FYY0

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	B, D	4		N/A
Glycosylation Resources
GlyTouCan:  G87171PZ GlyCosmos:  G87171PZ GlyGen:  G87171PZ

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	C	3		N/A
Glycosylation Resources
GlyTouCan:  G96370VA GlyCosmos:  G96370VA GlyGen:  G96370VA

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IOD	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M
GOL	L [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	K [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 2 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900010	B, D	alpha-maltotetraose	Oligosaccharide / Substrate analog

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900009	C	alpha-maltotriose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.182 
• R-Value Work: 0.136 
• R-Value Observed: 0.138 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 169.26	α = 90
b = 81.24	β = 101.14
c = 58.23	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
DNA	data collection
XDS	data reduction
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-02-12 
Deposition Author(s): Sim, L., Windahl, M.S., Moeller, M.S., Henriksen, A.

Revision History  

• Version 1.0: 2014-02-12
  Type: Initial release
  
• Version 1.1: 2015-10-14
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
• Version 2.1: 2023-11-08
  Changes: Data collection, Database references, Refinement description, Structure summary