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- PDB-6inc: Crystal structure of an acetolactate decarboxylase from Klebsiell... -

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Basic information

Entry
Database: PDB / ID: 6inc
TitleCrystal structure of an acetolactate decarboxylase from Klebsiella pneumoniae
ComponentsAlpha-acetolactate decarboxylase
KeywordsUNKNOWN FUNCTION / Acetolactate 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 pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.604 Å
AuthorsWu, W. / Zhang, Q. / Bartlam, M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31570128 China
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2019
Title: Structural characterization of an acetolactate decarboxylase from Klebsiella pneumoniae
Authors: Wu, W. / Zhao, Q. / Che, S. / Jia, H. / Liang, H. / Zhang, H. / Liu, R. / Zhang, Q. / Bartlam, M.
History
DepositionOct 24, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 16, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5107
Polymers29,2271
Non-polymers2836
Water4,648258
1
A: Alpha-acetolactate decarboxylase
hetero molecules

A: Alpha-acetolactate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,02014
Polymers58,4532
Non-polymers56712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Buried area3670 Å2
ΔGint-148 kcal/mol
Surface area17940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.152, 55.152, 119.377
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-594-

HOH

21A-634-

HOH

31A-652-

HOH

41A-657-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Alpha-acetolactate decarboxylase / BudA


Mass: 29226.637 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: budA, BN49_3166 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: W9BHF3, acetolactate decarboxylase

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Non-polymers , 5 types, 264 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 258 / 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: 1.79 Å3/Da / Density % sol: 31.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20% (w/v) PEG-3000, 0.1M citrate, pH 5.5 and 12% w/v Polyethylene glycol 3,350, 0.1M sodium malonate, pH 6.0 respectively

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 28357 / % possible obs: 99.9 % / Redundancy: 9.2 % / Rpim(I) all: 0.034 / Net I/σ(I): 21.1
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 9.8 % / Mean I/σ(I) obs: 5.8 / Num. unique obs: 1389 / Rpim(I) all: 0.165 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.14rc3_3199: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BT2

4bt2


Resolution: 1.604→27.576 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 15.39
RfactorNum. reflection% reflection
Rfree0.1796 1415 5 %
Rwork0.1523 --
obs0.1536 28295 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.604→27.576 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1742 0 12 258 2012
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091797
X-RAY DIFFRACTIONf_angle_d1.0652435
X-RAY DIFFRACTIONf_dihedral_angle_d14.1561059
X-RAY DIFFRACTIONf_chiral_restr0.063260
X-RAY DIFFRACTIONf_plane_restr0.007325
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.604-1.66140.19981220.16952665X-RAY DIFFRACTION100
1.6614-1.72790.22281440.16132634X-RAY DIFFRACTION100
1.7279-1.80650.17781470.15712626X-RAY DIFFRACTION100
1.8065-1.90170.17721630.14612646X-RAY DIFFRACTION100
1.9017-2.02080.14711200.13442664X-RAY DIFFRACTION100
2.0208-2.17680.17671430.13832647X-RAY DIFFRACTION100
2.1768-2.39570.16221510.14372703X-RAY DIFFRACTION100
2.3957-2.74210.17471430.15322695X-RAY DIFFRACTION100
2.7421-3.45370.17491510.15482721X-RAY DIFFRACTION100
3.4537-27.58010.19651310.16062879X-RAY DIFFRACTION100

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