3DC0 | pdb_00003dc0

Crystal structure of native alpha-amylase from Bacillus sp. KR-8104

• PDB DOI: https://doi.org/10.2210/pdb3DC0/pdb

• Classification: HYDROLASE
• Organism(s): Bacillus sp. KR-8104
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2008-06-03 Released: 2008-06-17 
• Deposition Author(s): Alikhajeh, J., Khajeh, K., Ranjbar, B., Naderi-Manesh, M., Naderi-Manesh, H., Chen, C.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.78 Å
• R-Value Free: 
  0.233 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.200 (DCC) 

Starting Model: experimental

Literature

Crystal structure of native alpha-amylase from Bacillus sp. KR-8104.

Alikhajeh, J., Khajeh, K., Ranjbar, B., Naderi-Manesh, M., Naderi-Manesh, H., Chen, C.J.

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: 46.76 kDa 
• Atom Count: 3,435 
• Modeled Residue Count: 422 
• Deposited Residue Count: 422 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
alpha-amylase	A	422	Bacillus sp. KR-8104	Mutation(s): 0  EC: 3.2.1.1
UniProt
Find proteins for B3GQD0 (Bacillus sp. KR-8104) Explore B3GQD0  Go to UniProtKB:  B3GQD0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	B [auth A], C [auth A], D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.78 Å
• R-Value Free:  0.233 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.200 (DCC) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 140.176	α = 90
b = 163.141	β = 90
c = 73.989	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-06-17 
Deposition Author(s): Alikhajeh, J., Khajeh, K., Ranjbar, B., Naderi-Manesh, M., Naderi-Manesh, H., Chen, C.J.

Revision History  

• Version 1.0: 2008-06-17
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-08-14
  Changes: Database references