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

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Basic information

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


acetyl-CoA C-acyltransferase activity / phenylacetate catabolic process / fatty acid beta-oxidation
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, 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
Probable acyl-CoA thiolase
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 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)86,7615
Polymers86,4842
Non-polymers2763
Water4,270237
1
A: Thiolase
B: Thiolase
hetero molecules

A: Thiolase
B: Thiolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,52110
Polymers172,9694
Non-polymers5536
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-y,z1
Buried area18430 Å2
ΔGint-34 kcal/mol
Surface area51120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)177.372, 177.372, 70.588
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41

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Components

#1: Protein Thiolase


Mass: 43242.180 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: PA3589 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9HY37
#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.: 237 / 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: 3.21 Å3/Da / Density % sol: 61.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 40% (v/v) 1,2-Propanediol 100 mM Sodium citrate/citric acid, pH 5.5 5% (w/v) PEG 1K

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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: May 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 54894 / % possible obs: 99.4 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.064 / Rrim(I) all: 0.129 / Χ2: 4.36 / Net I/σ(I): 10.7 / Num. measured all: 212439
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.2-2.243.60.30127240.9330.180.3521.38799.7
2.24-2.283.70.25827110.9390.1540.3021.54899.7
2.28-2.323.70.24527370.9510.1460.2861.7199.7
2.32-2.373.70.22727630.9590.1360.2661.74999.6
2.37-2.423.70.22327180.950.1320.261.80499.7
2.42-2.483.70.20827280.9570.1230.2421.80999.7
2.48-2.543.80.18727680.9620.1090.2172.165100
2.54-2.613.80.16927470.970.0990.1962.2499.9
2.61-2.693.90.15927470.9720.0920.1852.26599.8
2.69-2.773.90.14527350.9720.0840.1682.67899.8
2.77-2.873.90.13727800.9760.0780.1582.71799.8
2.87-2.9940.12527150.9790.0720.1443.06799.8
2.99-3.1240.11727340.9770.0670.1353.37999.8
3.12-3.2940.10627680.9820.0610.1234.05799.9
3.29-3.494.10.09827760.9830.0560.1134.28699.9
3.49-3.764.10.09527560.9830.0540.115.91499.8
3.76-4.144.10.09227940.9810.0530.1067.52199.6
4.14-4.7440.09427030.9760.0540.10910.73397.9
4.74-5.9740.09627930.980.0540.1110.63699.4
5.97-503.80.10226970.9610.0590.11913.91193.9

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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: 1ULQ

1ulq


Resolution: 2.21→40.39 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.927 / SU B: 4.849 / SU ML: 0.121 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.186 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2141 2757 5 %RANDOM
Rwork0.1742 ---
obs0.1762 52135 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 113.48 Å2 / Biso mean: 35.441 Å2 / Biso min: 17.41 Å2
Baniso -1Baniso -2Baniso -3
1-1.92 Å2-0 Å2-0 Å2
2--1.92 Å2-0 Å2
3----3.85 Å2
Refinement stepCycle: final / Resolution: 2.21→40.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5905 0 18 237 6160
Biso mean--52.36 41.47 -
Num. residues----801
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0136000
X-RAY DIFFRACTIONr_bond_other_d0.0010.0145903
X-RAY DIFFRACTIONr_angle_refined_deg1.7141.6358115
X-RAY DIFFRACTIONr_angle_other_deg1.3511.57513464
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0845799
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.75319.415342
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.19815957
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8511579
X-RAY DIFFRACTIONr_chiral_restr0.0780.2769
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026992
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021438
LS refinement shellResolution: 2.21→2.265 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.249 210 -
Rwork0.222 3737 -
obs--98.11 %

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