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- PDB-4nzs: Crystal structure of beta-ketothiolase BktB B from Ralstonia eutr... -

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Basic information

Entry
Database: PDB / ID: 4nzs
TitleCrystal structure of beta-ketothiolase BktB B from Ralstonia eutropha H16
ComponentsBeta-ketothiolase BktB
KeywordsTRANSFERASE / thiolase superfamily
Function / homology
Function and homology information


acetyl-CoA C-acyltransferase / acetyl-CoA C-acetyltransferase / acetyl-CoA C-acetyltransferase activity
Similarity search - Function
Thiolase, active site / Thiolases active site. / Thiolase, acyl-enzyme intermediate active site / Thiolases acyl-enzyme intermediate signature. / Thiolase / Thiolase, C-terminal / Thiolase, C-terminal domain / Thiolase, N-terminal / Thiolase, N-terminal domain / Thiolase/Chalcone synthase ...Thiolase, active site / Thiolases active site. / Thiolase, acyl-enzyme intermediate active site / Thiolases acyl-enzyme intermediate signature. / Thiolase / Thiolase, C-terminal / Thiolase, C-terminal domain / Thiolase, N-terminal / Thiolase, N-terminal domain / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Thiolase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Beta-ketothiolase BktB
Similarity search - Component
Biological speciesRalstonia eutropha (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.29 Å
AuthorsKim, E.J. / Son, H. / Kim, S. / Kim, K.J.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2014
Title: Crystal structure and biochemical characterization of beta-keto thiolase B from polyhydroxyalkanoate-producing bacterium Ralstonia eutropha H16
Authors: Kim, E.J. / Son, H.F. / Kim, S. / Ahn, J.W. / Kim, K.J.
History
DepositionDec 12, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 19, 2014Provider: repository / Type: Initial release
Revision 2.0Nov 22, 2017Group: Atomic model / Derived calculations / Refinement description
Category: atom_site / pdbx_struct_sheet_hbond ...atom_site / pdbx_struct_sheet_hbond / software / struct_conf / struct_sheet / struct_sheet_order / struct_sheet_range
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _struct_conf.pdbx_PDB_helix_id
Revision 2.1Nov 8, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-ketothiolase BktB
B: Beta-ketothiolase BktB


Theoretical massNumber of molelcules
Total (without water)83,3012
Polymers83,3012
Non-polymers00
Water25214
1
A: Beta-ketothiolase BktB
B: Beta-ketothiolase BktB

A: Beta-ketothiolase BktB
B: Beta-ketothiolase BktB


Theoretical massNumber of molelcules
Total (without water)166,6024
Polymers166,6024
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area14340 Å2
ΔGint-67 kcal/mol
Surface area53150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.954, 107.236, 144.137
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Beta-ketothiolase BktB / Acetyl-CoA acetyltransferase / Acetyl-CoA acyltransferase


Mass: 41650.430 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ralstonia eutropha (bacteria) / Strain: ATCC 17699 / H16 / DSM 428 / Stanier 337 / Gene: bktB, H16_A1445 / Plasmid: pProEX HTa / Production host: Escherichia coli (E. coli) / Strain (production host): B834
References: UniProt: Q0KBP1, acetyl-CoA C-acyltransferase, acetyl-CoA C-acetyltransferase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 2.52 Å3/Da / Density % sol: 51.25 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG3350, Li2SO4, pH 6.5, vapor diffusion, hanging drop, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97985 Å
DetectorType: Quantum 270 / Detector: CCD / Date: Mar 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97985 Å / Relative weight: 1
ReflectionResolution: 2.29→35.74 Å / Num. obs: 31979

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DLU

1dlu


Resolution: 2.29→35.74 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.872 / Occupancy max: 1 / Occupancy min: 1 / SU B: 14.18 / SU ML: 0.328 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.508 / ESU R Free: 0.349 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3189 1570 4.9 %RANDOM
Rwork0.2532 ---
obs0.2654 31979 85.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 135.81 Å2 / Biso mean: 58.836 Å2 / Biso min: 17.47 Å2
Baniso -1Baniso -2Baniso -3
1--2.95 Å20 Å20 Å2
2--2.2 Å2-0 Å2
3---0.75 Å2
Refinement stepCycle: LAST / Resolution: 2.29→35.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5718 0 0 14 5732
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0195799
X-RAY DIFFRACTIONr_bond_other_d0.0020.025728
X-RAY DIFFRACTIONr_angle_refined_deg1.7321.9617862
X-RAY DIFFRACTIONr_angle_other_deg0.886313098
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.25784
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.61823.478230
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.56915934
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0041550
X-RAY DIFFRACTIONr_chiral_restr0.0880.2922
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216732
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021266
X-RAY DIFFRACTIONr_mcbond_it4.4115.763142
X-RAY DIFFRACTIONr_mcbond_other4.4115.7583141
X-RAY DIFFRACTIONr_mcangle_it6.6178.6243924
LS refinement shellResolution: 2.29→2.353 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.442 101 -
Rwork0.404 1958 -
all-2059 -
obs--76.54 %

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