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- PDB-5xyj: Purification,crystallization and structural analysis of cytoplast... -

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Basic information

Entry
Database: PDB / ID: 5xyj
TitlePurification,crystallization and structural analysis of cytoplastic acetoacetyl-CoA thiolase from Saccharomyces cerevisiae
ComponentsAcetyl-CoA acetyltransferase
KeywordsTRANSFERASE / Acetoacetyl-CoA thiolase / Claisen condension / The mevalonate pathway
Function / homology
Function and homology information


Cholesterol biosynthesis / ergosterol biosynthetic process / acetyl-CoA C-acetyltransferase / acetyl-CoA C-acetyltransferase activity / vacuole / mitochondrion / metal ion binding / nucleus / cytosol / 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 speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsZhou, P.F.
CitationJournal: To Be Published
Title: Purification,crystallization and structural analysis of cytoplastic acetoacetyl-CoA thiolase from Saccharomyces cerevisiae
Authors: Zhou, P.F.
History
DepositionJul 8, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 11, 2018Provider: 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 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Acetyl-CoA acetyltransferase
A: Acetyl-CoA acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,9944
Polymers85,8092
Non-polymers1842
Water14,574809
1
B: Acetyl-CoA acetyltransferase
A: Acetyl-CoA acetyltransferase
hetero molecules

B: Acetyl-CoA acetyltransferase
A: Acetyl-CoA acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,9878
Polymers171,6194
Non-polymers3684
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
Buried area15080 Å2
ΔGint-51 kcal/mol
Surface area52220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.804, 89.250, 119.189
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-780-

HOH

21B-835-

HOH

31A-572-

HOH

41A-729-

HOH

51A-744-

HOH

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Components

#1: Protein Acetyl-CoA acetyltransferase / Acetoacetyl-CoA thiolase / Ergosterol biosynthesis protein 10


Mass: 42904.723 Da / Num. of mol.: 2 / Mutation: C91A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: ERG10, YPL028W, LPB3 / Plasmid: pET22bN / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P41338, 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.: 809 / 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: 2.34 Å3/Da / Density % sol: 47.47 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop
Details: 0.2M ammonium citrate (pH 6.5), polyethylene glycol 3350 (19%)
PH range: 6.5-7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97778 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97778 Å / Relative weight: 1
ReflectionResolution: 1.93→50 Å / Num. obs: 62459 / % possible obs: 98.8 % / Redundancy: 8.8 % / Biso Wilson estimate: 15.6 Å2 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.034 / Χ2: 1 / Net I/σ(I): 18.7
Reflection shellResolution: 1.93→1.98 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.515 / Mean I/σ(I) obs: 5.1 / Num. unique obs: 3038 / CC1/2: 0.946 / Rpim(I) all: 0.183 / Χ2: 0.987 / % possible all: 98.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
HKL-3000v715data reduction
HKL-2000v715data scaling
MOLREPv7.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2IB7

2ib7


Resolution: 1.93→47.53 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.607 / SU ML: 0.075 / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17181 3263 5.2 %RANDOM
Rwork0.15572 ---
obs0.15655 59159 97.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.4 Å2-0 Å2-0 Å2
2---1.41 Å20 Å2
3---1.01 Å2
Refinement stepCycle: 1 / Resolution: 1.93→47.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5834 0 12 809 6655
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0195934
X-RAY DIFFRACTIONr_bond_other_d0.0060.025846
X-RAY DIFFRACTIONr_angle_refined_deg1.2521.9628034
X-RAY DIFFRACTIONr_angle_other_deg0.902313458
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6155790
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.81125.652230
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.541151002
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5481522
X-RAY DIFFRACTIONr_chiral_restr0.070.2936
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216830
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021248
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.926→1.976 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.235 179 -
Rwork0.195 3315 -
obs--74.44 %

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