3VU2

Structure of the Starch Branching Enzyme I (BEI) complexed with maltopentaose from Oryza sativa L

• PDB DOI: https://doi.org/10.2210/pdb3VU2/pdb

• Classification: TRANSFERASE
• Organism(s): Oryza sativa Japonica Group
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2012-06-14 Released: 2013-05-08 
• Deposition Author(s): Chaen, K., Kakuta, Y., Kimura, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.23 Å
• R-Value Free: 0.286 
• R-Value Work: 0.226 
• R-Value Observed: 0.229 

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)

Macromolecule Content

• Total Structure Weight: 165.24 kDa 
• Atom Count: 12,313 
• Modelled Residue Count: 1,383 
• Deposited Residue Count: 1,404 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
1,4-alpha-glucan-branching enzyme, chloroplastic/amyloplastic	A, B	702	Oryza sativa Japonica Group	Mutation(s): 1  Gene Names: SBE1, RBE1, Os06g0726400, LOC_Os06g51084, P0017G10.8-1, P0017G10.8-2, P0548E04.28-1, P0548E04.28-2 EC: 2.4.1.18
UniProt
Find proteins for Q01401 (Oryza sativa subsp. japonica) Explore Q01401  Go to UniProtKB:  Q01401

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-(1-4)-alpha-D-glucopyranose	C, D	5		N/A
Glycosylation Resources
GlyTouCan:  G50146AM GlyCosmos:  G50146AM

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BGC	E [auth A], F [auth A], H [auth B], I [auth B]	beta-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-VFUOTHLCSA-N
GOL	G [auth A], J [auth B], K [auth B], L [auth B], M [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900030	C, D	alpha-maltopentaose	Oligosaccharide / Substrate analog

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.23 Å
• R-Value Free: 0.286 
• R-Value Work: 0.226 
• R-Value Observed: 0.229 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.81	α = 90
b = 66.56	β = 89.97
c = 169.625	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-05-08 
Deposition Author(s): Chaen, K., Kakuta, Y., Kimura, M.

Revision History  

• Version 1.0: 2013-05-08
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2024-03-20
  Changes: Data collection, Database references, Structure summary