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- PDB-6j92: Crystal structure of acetolactate decarboxylase from Enterbacter ... -

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Basic information

Entry
Database: PDB / ID: 6j92
TitleCrystal structure of acetolactate decarboxylase from Enterbacter aerogenes
ComponentsAlpha-acetolactate decarboxylase
KeywordsLYASE / decarboxylase
Function / homology
Function and homology information


acetolactate decarboxylase / acetoin biosynthetic process / acetolactate decarboxylase activity
Similarity search - Function
Alpha-acetolactate decarboxylase / Alpha-acetolactate decarboxylase / Hypothetical protein, similar to alpha- acetolactate decarboxylase; domain 2 / 60s Ribosomal Protein L30; Chain: A; / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Alpha-acetolactate decarboxylase
Similarity search - Component
Biological speciesKlebsiella aerogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.421 Å
AuthorsMingyang, L. / Song, X. / Ji, F. / Feng, Y.
CitationJournal: To Be Published
Title: Crystal structure of acetolactate decarboxylase from Enterbacter aerogenes
Authors: Ji, F. / Feng, Y. / Mingyang, L.
History
DepositionJan 21, 2019Deposition site: PDBJ / Processing site: PDBJ
SupersessionJan 22, 2020ID: 5YHK
Revision 1.0Jan 22, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: audit_author / chem_comp_atom ...audit_author / chem_comp_atom / chem_comp_bond / citation_author / database_2 / pdbx_initial_refinement_model
Item: _audit_author.name / _citation_author.name ..._audit_author.name / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha-acetolactate decarboxylase
B: Alpha-acetolactate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5416
Polymers53,3402
Non-polymers2024
Water2,090116
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, DIMER
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2400 Å2
ΔGint-122 kcal/mol
Surface area17450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.541, 83.541, 139.173
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Alpha-acetolactate decarboxylase


Mass: 26669.805 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella aerogenes (bacteria) / Gene: aldC / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P05361, acetolactate decarboxylase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Zn
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 45.96 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 20%(v/v)1,4-Butanediol, 100mM Sodium acetate/Acetic acid pH4.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9798 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Jun 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 2.42→50 Å / Num. obs: 19453 / % possible obs: 99.88 % / Redundancy: 12.2 % / Biso Wilson estimate: 38.03 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.104 / Net I/σ(I): 30.16
Reflection shellResolution: 2.42→2.51 Å / Redundancy: 11.7 % / Rmerge(I) obs: 0.5849 / Mean I/σ(I) obs: 7.21 / Num. unique obs: 1906 / CC1/2: 0.93 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XNE

5xne


Resolution: 2.421→45.034 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.31
RfactorNum. reflection% reflection
Rfree0.2185 929 4.78 %
Rwork0.1726 --
obs0.1748 19445 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.421→45.034 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3501 0 4 116 3621
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093586
X-RAY DIFFRACTIONf_angle_d1.2054867
X-RAY DIFFRACTIONf_dihedral_angle_d15.5441308
X-RAY DIFFRACTIONf_chiral_restr0.049525
X-RAY DIFFRACTIONf_plane_restr0.005653
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4207-2.54840.32391280.22452570X-RAY DIFFRACTION99
2.5484-2.7080.24081440.20252590X-RAY DIFFRACTION100
2.708-2.91710.24861190.19272596X-RAY DIFFRACTION100
2.9171-3.21050.25331480.18572608X-RAY DIFFRACTION100
3.2105-3.67490.23491210.16772646X-RAY DIFFRACTION100
3.6749-4.62930.15911350.15072672X-RAY DIFFRACTION100
4.6293-45.04170.21441340.16472834X-RAY DIFFRACTION100

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