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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.191 (Depositor), 0.194 (DCC)
R-Value Work:
0.171 (Depositor), 0.177 (DCC)
R-Value Observed:
0.172 (Depositor)

Starting Model: experimental
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This is version 1.2 of the entry. See complete history.

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

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

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	E0U503
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.191 (Depositor), 0.194 (DCC)
R-Value Work: 0.171 (Depositor), 0.177 (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

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Entry History

Deposition Data

Released Date: 2019-11-13

Deposition Author(s):

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.