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

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Basic information

Entry
Database: PDB / ID: 6inb
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: 1.8 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)29,3273
Polymers29,2271
Non-polymers1012
Water3,549197
1
A: Alpha-acetolactate decarboxylase
hetero molecules

A: Alpha-acetolactate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,6556
Polymers58,4532
Non-polymers2024
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Buried area2490 Å2
ΔGint-111 kcal/mol
Surface area17920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.279, 55.279, 119.532
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-595-

HOH

21A-597-

HOH

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Components

#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
#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.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / 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: 1.8 Å3/Da / Density % sol: 31.81 %
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

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9785 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: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 20250 / % possible obs: 100 % / Redundancy: 19 % / Rpim(I) all: 0.021 / Net I/σ(I): 27.8
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 15 % / Mean I/σ(I) obs: 9.5 / Num. unique obs: 999 / Rpim(I) all: 0.09 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BT2

4bt2


Resolution: 1.8→47.87 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.93 / SU B: 4.644 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.131 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21914 1006 5 %RANDOM
Rwork0.17272 ---
obs0.17497 19193 99.88 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.88 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å2-0.03 Å2-0 Å2
2---0.05 Å20 Å2
3---0.17 Å2
Refinement stepCycle: 1 / Resolution: 1.8→47.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1750 0 2 197 1949
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0131799
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171595
X-RAY DIFFRACTIONr_angle_refined_deg1.5631.6432442
X-RAY DIFFRACTIONr_angle_other_deg1.3881.5733700
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9265220
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.55322.11109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.03415287
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7761513
X-RAY DIFFRACTIONr_chiral_restr0.0660.2226
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022054
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02401
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7171.125877
X-RAY DIFFRACTIONr_mcbond_other0.7131.124876
X-RAY DIFFRACTIONr_mcangle_it1.1681.6831095
X-RAY DIFFRACTIONr_mcangle_other1.1681.6851096
X-RAY DIFFRACTIONr_scbond_it1.1261.273922
X-RAY DIFFRACTIONr_scbond_other1.1251.274923
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.7741.8611347
X-RAY DIFFRACTIONr_long_range_B_refined5.314.9581992
X-RAY DIFFRACTIONr_long_range_B_other5.15814.2111948
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.802→1.849 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.234 67 -
Rwork0.175 1393 -
obs--99.12 %
Refinement TLS params.Method: refined / Origin x: -7.049 Å / Origin y: 17.131 Å / Origin z: 45.132 Å
111213212223313233
T0.008 Å2-0.0062 Å2-0.0048 Å2-0.0306 Å2-0.0082 Å2--0.0151 Å2
L1.3803 °2-0.5881 °2-0.2187 °2-1.6757 °2-0.1356 °2--1.8691 °2
S0.0004 Å °0.0397 Å °-0.0328 Å °-0.0168 Å °0.0024 Å °0.0987 Å °0.1029 Å °-0.1445 Å °-0.0028 Å °

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