3VOC | pdb_00003voc

Crystal structure of the catalytic domain of beta-amylase from paenibacillus polymyxa

• PDB DOI: https://doi.org/10.2210/pdb3VOC/pdb

• Classification: HYDROLASE
• Organism(s): Paenibacillus polymyxa
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-01-21 Released: 2013-02-20 
• Deposition Author(s): Nishimura, S., Fujioka, T., Nakaniwa, T., Tada, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.190 (Depositor), 0.193 (DCC) 
• R-Value Work: 
  0.153 (Depositor), 0.155 (DCC) 
• R-Value Observed: 
  0.155 (Depositor) 

Starting Model: experimental

Literature

Structural analysis by X-ray crystallography and small-angle scattering of the multi-domain beta-amylase from Paenibacillus polymyxa

Nishimura, S., Fujioka, T., Takahashi, R., Nakaniwa, T., Fukada, H., Inui, T., Tada, T., Kawaguchi, T., Sumitani, 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: 46.74 kDa 
• Atom Count: 3,608 
• Modeled Residue Count: 416 
• Deposited Residue Count: 419 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta/alpha-amylase	A	419	Paenibacillus polymyxa	Mutation(s): 0  EC: 3.2.1.2 (PDB Primary Data), 3.2.1.1 (UniProt)
UniProt
Find proteins for P21543 (Paenibacillus polymyxa) Explore P21543  Go to UniProtKB:  P21543

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TRS	J [auth A], K [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
PEG	L [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL	G [auth A], H [auth A], I [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	D [auth A], E [auth A], F [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.190 (Depositor), 0.193 (DCC) 
• R-Value Work:  0.153 (Depositor), 0.155 (DCC) 
• R-Value Observed: 0.155 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.028	α = 90
b = 68.519	β = 90
c = 93.904	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-02-20 
Deposition Author(s): Nishimura, S., Fujioka, T., Nakaniwa, T., Tada, T.

Revision History  

• Version 1.0: 2013-02-20
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-10-30
  Changes: Structure summary