3VX1 | pdb_00003vx1

Crystal Structure of alpha-Amylase from Aspergillus oryzae

• PDB DOI: https://doi.org/10.2210/pdb3VX1/pdb

• Classification: HYDROLASE
• Organism(s): Aspergillus oryzae RIB40
• Mutation(s): No 


• Deposited: 2012-09-06 Released: 2013-09-11 
• Deposition Author(s): Sugahara, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.247 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.208 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.208 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of alpha-Amylase from Aspergillus oryzae

Sugahara, M.

To be published.

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: 52.79 kDa 
• Atom Count: 4,006 
• Modelled Residue Count: 477 
• Deposited Residue Count: 478 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-amylase A type-1/2	A	478	Aspergillus oryzae RIB40	Mutation(s): 0  EC: 3.2.1.1
UniProt
Find proteins for P0C1B3 (Aspergillus oryzae (strain ATCC 42149 / RIB 40)) Explore P0C1B3  Go to UniProtKB:  P0C1B3
Glycosylation
Glycosylation Sites: 1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	B [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
CA	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.247 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.208 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.208 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.368	α = 90
b = 66.678	β = 90
c = 131.551	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-09-11 
Deposition Author(s): Sugahara, M.

Revision History  

• Version 1.0: 2013-09-11
  Type: Initial release
  
• Version 1.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 1.3: 2024-10-30
  Changes: Structure summary