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- PDB-4o99: Crystal structure of Beta-ketothiolase (PhaA) from Ralstonia eutr... -

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Basic information

Entry
Database: PDB / ID: 4o99
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, acyl-enzyme intermediate active site / Thiolases acyl-enzyme intermediate signature. / Thiolase, conserved site / Thiolases signature 2. / Thiolase, C-terminal / Thiolase, C-terminal domain / Thiolase / Thiolase, N-terminal ...Thiolase, active site / Thiolases active site. / Thiolase, acyl-enzyme intermediate active site / Thiolases acyl-enzyme intermediate signature. / Thiolase, conserved site / Thiolases signature 2. / 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: 1.96 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 1.0Dec 17, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,0356
Polymers161,8514
Non-polymers1842
Water18,1231006
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14180 Å2
ΔGint-56 kcal/mol
Surface area50500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.377, 105.474, 106.914
Angle α, β, γ (deg.)90.000, 106.180, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 40462.625 Da / Num. of mol.: 4
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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1006 / 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: 2.29 Å3/Da / Density % sol: 46.23 %
Crystal growTemperature: 295 K / Method: hanging drop / pH: 8.5
Details: 20% PEG MME 2K, Tris-HCl, 0.2M Trimethylamine N-oxide dihydrate, pH 8.5, 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 270r / Detector: CCD / Date: Jul 3, 2013 / Details: Rh coated Torroidal Mirror
RadiationMonochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97954 Å / Relative weight: 1
ReflectionResolution: 1.96→30.62 Å / Num. obs: 98053

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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: 1.96→30.62 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.903 / Occupancy max: 1 / Occupancy min: 1 / SU B: 3.507 / SU ML: 0.101 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.185 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
RfactorNum. reflection% reflectionSelection details
Rfree0.23 4901 5 %RANDOM
Rwork0.171 ---
obs0.174 98053 94.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 94.48 Å2 / Biso mean: 22.6782 Å2 / Biso min: 10.55 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å2-0 Å2
2---0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.96→30.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11307 0 12 1006 12325
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.01911477
X-RAY DIFFRACTIONr_bond_other_d0.0010.0211460
X-RAY DIFFRACTIONr_angle_refined_deg1.8171.97115520
X-RAY DIFFRACTIONr_angle_other_deg0.888326368
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.24951564
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.48725.248404
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.693151952
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0441556
X-RAY DIFFRACTIONr_chiral_restr0.1110.21802
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02113200
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022316
X-RAY DIFFRACTIONr_mcbond_it1.6971.9876268
X-RAY DIFFRACTIONr_mcbond_other1.6961.9876267
X-RAY DIFFRACTIONr_mcangle_it2.3742.977828
LS refinement shellResolution: 1.964→2.014 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 369 -
Rwork0.195 6926 -
all-7295 -
obs--95.7 %

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