6J3D | pdb_00006j3d

Crystal structure of acetolactate decarboxylase from Bacillus subtilis subspecies spizizenii in space group P21212

• PDB DOI: https://doi.org/10.2210/pdb6J3D/pdb

• Classification: LYASE
• Organism(s): Bacillus spizizenii str. W23
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-01-04 Released: 2019-11-13 
• Deposition Author(s): Yoon, S.I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.191 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.171 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.172 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of alpha-acetolactate decarboxylase from Bacillus subtilis subspecies spizizeni.

Eom, J., Oh, H.B., Yoon, S.I.

(2019) Korean J Microbiol 55: 9-16

• DOI: https://doi.org/10.7845/kjm.2019.9005

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 58.75 kDa 
• Atom Count: 4,017 
• Modeled Residue Count: 465 
• Deposited Residue Count: 522 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-acetolactate decarboxylase	A, B	261	Bacillus spizizenii str. W23	Mutation(s): 0  Gene Names: alsD, BSUW23_17695 EC: 4.1.1.5
UniProt
Find proteins for E0U503 (Bacillus spizizenii (strain ATCC 23059 / NRRL B-14472 / W23)) Explore E0U503  Go to UniProtKB:  E0U503

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A], D [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.191 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.171 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.172 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.276	α = 90
b = 129.643	β = 90
c = 45.721	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-11-13 
Deposition Author(s): Yoon, S.I.

Revision History  

• Version 1.0: 2019-11-13
  Type: Initial release
  
• Version 1.1: 2019-11-20
  Changes: Database references
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Derived calculations, Refinement description