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- PDB-8gqj: Structure of Thiolase from Pseudomonas aeruginosa PAO1 -

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Basic information

Entry
Database: PDB / ID: 8gqj
TitleStructure of Thiolase from Pseudomonas aeruginosa PAO1
ComponentsThiolase
KeywordsTRANSFERASE / acetyl-CoA acetyltransferase thiolase
Function / homology
Function and homology information


acetyl-CoA C-acetyltransferase / acetyl-CoA C-acetyltransferase activity / fatty acid metabolic process / 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-like
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / Acetyl-CoA acetyltransferase
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,3718
Polymers87,3792
Non-polymers9916
Water11,584643
1
A: Thiolase
B: Thiolase
hetero molecules

A: Thiolase
B: Thiolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,74116
Polymers174,7594
Non-polymers1,98212
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_555-x,-x+y,-z1
Buried area18350 Å2
ΔGint-48 kcal/mol
Surface area48600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)173.201, 173.201, 139.692
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein Thiolase


Mass: 43689.730 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: atoB, PA2001 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9I2A8, acetyl-CoA C-acetyltransferase
#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: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-2PE / NONAETHYLENE GLYCOL


Mass: 414.488 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H38O10 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 643 / 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: 3.46 Å3/Da / Density % sol: 64.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 12% (w/v) PEG 3350 4% (v/v) Tacsimate, pH 8.0

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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: Jun 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.78→50 Å / Num. obs: 113500 / % possible obs: 98.1 % / Redundancy: 13 % / Rmerge(I) obs: 0.161 / Rpim(I) all: 0.039 / Rrim(I) all: 0.166 / Χ2: 4.306 / Net I/σ(I): 9.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.8-1.8370.29755080.7930.1010.3161.33596.3
1.83-1.867.60.2954500.8480.0950.3071.47696.3
1.86-1.98.20.28255420.8910.0880.2961.6196.8
1.9-1.948.60.27455300.9190.0840.2881.76797.3
1.94-1.989.60.26456000.9370.0770.2761.98397.5
1.98-2.0310.60.24955880.960.070.2592.25398
2.03-2.08110.23856120.9680.0650.2472.33598.1
2.08-2.1311.60.22556150.9780.060.2332.52298.1
2.13-2.212.10.21556520.980.0570.2232.68698.6
2.2-2.2712.70.20356320.9850.0520.212.88298.3
2.27-2.3513.50.19256740.9870.0480.1983.07498.7
2.35-2.4413.80.18556510.9890.0460.1913.16798.6
2.44-2.5514.20.17856970.990.0440.1843.27398.6
2.55-2.6914.90.1756960.9920.0410.1753.61798.7
2.69-2.8615.70.16357130.9920.0390.1674.09198.8
2.86-3.0816.30.15657340.9930.0360.164.81698.7
3.08-3.3917.40.14957620.9940.0340.1535.86798.8
3.39-3.8818.40.14558270.9940.0330.1497.3999.3
3.88-4.8818.70.14258740.9930.0320.1458.83898.9
4.88-5017.50.14461430.9920.0340.1488.17698.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4O99

4o99


Resolution: 1.78→32.75 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.739 / SU ML: 0.052 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.079 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1778 5678 5 %RANDOM
Rwork0.156 ---
obs0.1571 107817 97.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 96.49 Å2 / Biso mean: 17.436 Å2 / Biso min: 7.87 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20.08 Å20 Å2
2--0.15 Å20 Å2
3----0.5 Å2
Refinement stepCycle: final / Resolution: 1.78→32.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5664 0 52 646 6362
Biso mean--41.22 28.51 -
Num. residues----786
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0135784
X-RAY DIFFRACTIONr_bond_other_d0.0010.0155746
X-RAY DIFFRACTIONr_angle_refined_deg1.7381.6287813
X-RAY DIFFRACTIONr_angle_other_deg1.5051.57813176
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5315784
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.98821.832262
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.28415942
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7031544
X-RAY DIFFRACTIONr_chiral_restr0.0890.2766
X-RAY DIFFRACTIONr_gen_planes_refined0.010.026678
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021242
LS refinement shellResolution: 1.784→1.831 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 363 -
Rwork0.256 6815 -
all-7178 -
obs--84.41 %

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