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- PDB-4o9a: Crystal structure of Beta-ketothiolase (PhaA) from Ralstonia eutr... -

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Basic information

Entry
Database: PDB / ID: 4o9a
TitleCrystal structure of Beta-ketothiolase (PhaA) from Ralstonia eutropha H16
ComponentsAcetyl-CoA acetyltransferase
KeywordsTRANSFERASE / acetoacetyl-coa transferase / PHB biosynthesis / Acyltransferase Transferase
Function / homology
Function and homology information


poly-hydroxybutyrate biosynthetic process / acetyl-CoA C-acetyltransferase / acetyl-CoA C-acetyltransferase activity / cytoplasm
Similarity search - Function
Thiolase, active site / Thiolases active site. / Thiolase, conserved site / Thiolases signature 2. / Thiolase, acyl-enzyme intermediate active site / Thiolases acyl-enzyme intermediate signature. / Thiolase, C-terminal / Thiolase, C-terminal domain / Thiolase / Thiolase, N-terminal ...Thiolase, active site / Thiolases active site. / Thiolase, conserved site / Thiolases signature 2. / Thiolase, acyl-enzyme intermediate active site / Thiolases acyl-enzyme intermediate signature. / Thiolase, C-terminal / Thiolase, C-terminal domain / Thiolase / 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
Acetyl-CoA acetyltransferase
Similarity search - Component
Biological speciesRalstonia eutropha (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 Å
AuthorsKim, E.J. / Kim, J. / Kim, S. / Kim, K.J.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2014
Title: Crystal structure and biochemical characterization of PhaA from Ralstonia eutropha, a polyhydroxyalkanoate-producing bacterium.
Authors: Kim, E.J. / Kim, K.J.
History
DepositionJan 2, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 4, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 1.2Nov 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

Downloads & links

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Assembly

Deposited unit
A: Acetyl-CoA acetyltransferase
B: Acetyl-CoA acetyltransferase
C: Acetyl-CoA acetyltransferase
D: Acetyl-CoA acetyltransferase


Theoretical massNumber of molelcules
Total (without water)165,1024
Polymers165,1024
Non-polymers00
Water5,549308
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13500 Å2
ΔGint-56 kcal/mol
Surface area50850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.271, 104.705, 106.907
Angle α, β, γ (deg.)90.000, 106.120, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Acetyl-CoA acetyltransferase / Acetoacetyl-CoA thiolase


Mass: 41275.430 Da / Num. of mol.: 4 / Fragment: C88S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ralstonia eutropha (bacteria) / Strain: H16 / Gene: H16_A1438, phaA, phbA / Plasmid: pPROEXHTa / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: P14611, acetyl-CoA C-acetyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 308 / 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: 2.27 Å3/Da / Density % sol: 45.79 %
Crystal growTemperature: 295 K / Method: hanging drop / pH: 7.5
Details: 25% PEG 3350, HEPES, 0.2M Ammonium sulfate, pH 7.5, 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: 0.97954 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Sep 15, 2013 / Details: Rh coated Torroidal Mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97954 Å / Relative weight: 1
ReflectionResolution: 1.52→27.86 Å / Num. obs: 200802

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Processing

Software
NameVersionClassificationNB
REFMAC5.7.0032refinement
PDB_EXTRACT3.14data extraction
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DLU

1dlu


Resolution: 1.52→27.86 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.935 / Occupancy max: 1 / Occupancy min: 1 / SU B: 2.485 / SU ML: 0.085 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.099 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
RfactorNum. reflection% reflectionSelection details
Rfree0.2544 10085 5 %RANDOM
Rwork0.2176 ---
obs0.2194 200802 91.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 78.95 Å2 / Biso mean: 19.6175 Å2 / Biso min: 7.77 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å2-0 Å2-0 Å2
2--0.15 Å20 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.52→27.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11308 0 0 308 11616
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.01911468
X-RAY DIFFRACTIONr_bond_other_d0.0010.0211448
X-RAY DIFFRACTIONr_angle_refined_deg2.0211.97115512
X-RAY DIFFRACTIONr_angle_other_deg1.016326340
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.38851564
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.38425.248404
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.795151952
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.121556
X-RAY DIFFRACTIONr_chiral_restr0.1770.21800
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02113204
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022316
X-RAY DIFFRACTIONr_mcbond_it1.6271.7726268
X-RAY DIFFRACTIONr_mcbond_other1.6191.7716267
X-RAY DIFFRACTIONr_mcangle_it2.2792.6537828
LS refinement shellResolution: 1.522→1.562 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.42 558 -
Rwork0.393 11269 -
all-11827 -
obs--72.91 %

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