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- PDB-8gqf: Crystal structure of Thiolase -

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Basic information

Entry
Database: PDB / ID: 8gqf
TitleCrystal structure of Thiolase
ComponentsThiolase
KeywordsTRANSFERASE / acetyl-CoA acetyltransferase thiolase
Function / homology
Function and homology information


acetyl-CoA C-acyltransferase / acetyl-CoA C-acetyltransferase activity
Similarity search - Function
: / 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-like
Similarity search - Domain/homology
Acetyl-CoA C-acyltransferase
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsHong, J. / Son, H.F. / Kim, K.J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structure of thiolase from Pseudomonas aeruginosa PAO1
Authors: Hong, J. / Son, H.F. / Kim, K.J.
History
DepositionAug 30, 2022Deposition site: PDBJ / Processing site: RCSB
Revision 1.0Mar 13, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thiolase
B: Thiolase
C: Thiolase
D: Thiolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,2427
Polymers169,9664
Non-polymers2763
Water15,079837
1
A: Thiolase
D: Thiolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,1674
Polymers84,9832
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5660 Å2
ΔGint-23 kcal/mol
Surface area24370 Å2
MethodPISA
2
B: Thiolase
C: Thiolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,0753
Polymers84,9832
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5400 Å2
ΔGint-22 kcal/mol
Surface area24290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.562, 82.266, 97.739
Angle α, β, γ (deg.)90.010, 75.000, 89.950
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Thiolase


Mass: 42491.551 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0F7QQ39
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 837 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.31 Å3/Da / Density % sol: 46.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 4% (v/v) polyethylenime 100 mM Sodium citrate, pH 5.6 500 mM Sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 134796 / % possible obs: 96.6 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.056 / Rrim(I) all: 0.107 / Χ2: 3.781 / Net I/σ(I): 12.3 / Num. measured all: 462434
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.8-1.833.20.29466170.9010.1870.351.75295.2
1.83-1.863.20.27767000.920.1780.3311.75395.5
1.86-1.93.20.24666020.9290.1570.2931.69995.7
1.9-1.943.30.22367720.9340.1410.2641.85895.8
1.94-1.983.30.19666310.9570.1230.2321.94496
1.98-2.033.40.17367820.9630.1070.2042.22296.3
2.03-2.083.40.15566950.9680.0950.1832.59196.4
2.08-2.133.50.14567230.970.0890.1712.6396.5
2.13-2.23.40.13867970.9730.0840.1622.85396.6
2.2-2.273.50.12267490.9740.0740.1433.11196.9
2.27-2.353.40.11867570.9790.0720.1383.2796.7
2.35-2.443.40.10667240.9790.0650.1243.4596.9
2.44-2.553.50.10268120.9820.0620.1193.58797.2
2.55-2.693.50.09667920.970.0580.1124.04997.4
2.69-2.863.50.08768210.9760.0520.1024.12697.6
2.86-3.083.60.08167940.9880.0480.0944.74697.7
3.08-3.393.60.07568480.9890.0440.0875.24597.9
3.39-3.883.60.07568850.9850.0450.0876.57798.3
3.88-4.883.50.07866580.9790.0480.0929.20895.5
4.88-503.40.07966370.9760.0490.0937.66195.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ULQ

1ulq


Resolution: 1.8→31.49 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.932 / SU B: 3.024 / SU ML: 0.092 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.128 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2202 6597 4.9 %RANDOM
Rwork0.1808 ---
obs0.1828 128199 95.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 78.04 Å2 / Biso mean: 21.262 Å2 / Biso min: 10.09 Å2
Baniso -1Baniso -2Baniso -3
1-0.86 Å20.03 Å21.51 Å2
2---1.19 Å20.13 Å2
3---1 Å2
Refinement stepCycle: final / Resolution: 1.8→31.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10950 0 18 840 11808
Biso mean--33.25 29.44 -
Num. residues----1513
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01311117
X-RAY DIFFRACTIONr_bond_other_d0.0010.01510931
X-RAY DIFFRACTIONr_angle_refined_deg1.6911.6315054
X-RAY DIFFRACTIONr_angle_other_deg1.4361.57125044
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.06651509
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.20320.687524
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.195151785
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.38215100
X-RAY DIFFRACTIONr_chiral_restr0.080.21493
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212858
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022454
LS refinement shellResolution: 1.802→1.848 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 450 -
Rwork0.247 8420 -
all-8870 -
obs--85.42 %

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