3DHU | pdb_00003dhu

Crystal structure of an alpha-amylase from Lactobacillus plantarum

• PDB DOI: https://doi.org/10.2210/pdb3DHU/pdb

• Classification: HYDROLASE
• Organism(s): Lactiplantibacillus plantarum
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-06-18 Released: 2008-08-12 
• Deposition Author(s): Bonanno, J.B., Dickey, M., Bain, K.T., Iizuka, M., Ozyurt, S., Smith, D., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.251 (Depositor), 0.255 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.205 (DCC) 
• R-Value Observed: 
  0.203 (Depositor) 

Literature

Crystal structure of an alpha-amylase from Lactobacillus plantarum

Bonanno, J.B., Dickey, M., Bain, K.T., Iizuka, M., Ozyurt, S., Smith, D., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C.

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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 204.44 kDa 
• Atom Count: 14,732 
• Modeled Residue Count: 1,680 
• Deposited Residue Count: 1,796 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-amylase	A, B, C, D	449	Lactiplantibacillus plantarum	Mutation(s): 0  Gene Names: amy2, lp_0179 EC: 3.2.1.1
UniProt
Find proteins for F9USZ1 (Lactiplantibacillus plantarum (strain ATCC BAA-793 / NCIMB 8826 / WCFS1)) Explore F9USZ1  Go to UniProtKB:  F9USZ1

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.251 (Depositor), 0.255 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.205 (DCC) 
• R-Value Observed: 0.203 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 202.279	α = 90
b = 63.773	β = 102.93
c = 155.677	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
SHELXCD	phasing
SHELXE	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-08-12 
Deposition Author(s): Bonanno, J.B., Dickey, M., Bain, K.T., Iizuka, M., Ozyurt, S., Smith, D., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2008-08-12
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2018-11-14
  Changes: Data collection, Structure summary
• Version 1.4: 2021-02-10
  Changes: Database references, Structure summary
• Version 1.5: 2024-02-21
  Changes: Data collection, Database references