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

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Basic information

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


3-oxoadipyl-CoA thiolase / 3-oxoadipyl-CoA thiolase activity / acetyl-CoA C-acyltransferase activity / 3,4-dihydroxybenzoate catabolic process / beta-ketoadipate pathway / phenylacetate catabolic process / fatty acid beta-oxidation
Similarity search - Function
Beta-ketoadipyl CoA thiolase / : / 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 ...Beta-ketoadipyl CoA thiolase / : / 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-like
Similarity search - Domain/homology
Beta-ketoadipyl-CoA thiolase
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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)173,2698
Polymers172,9014
Non-polymers3684
Water12,196677
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17530 Å2
ΔGint-48 kcal/mol
Surface area51180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.337, 128.356, 151.970
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Thiolase


Mass: 43225.227 Da / Num. of mol.: 4
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: pcaF, PA0228 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9I6R0, 3-oxoadipyl-CoA thiolase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 677 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.06 Å3/Da / Density % sol: 59.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 12% (w/v) PEG 20K 100 mM MES, pH 6.5

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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: 106966 / % possible obs: 99.3 % / Redundancy: 7.7 % / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.038 / Rrim(I) all: 0.108 / Χ2: 2.395 / Net I/σ(I): 10.6 / Num. measured all: 820894
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.2-2.247.30.28152210.9720.1090.3021.86497.7
2.24-2.287.30.27551860.9740.1060.2951.89197.8
2.28-2.327.30.24851990.9770.0950.2671.90798.1
2.32-2.377.40.23552880.9810.090.2531.93198.8
2.37-2.427.50.22153000.9820.0850.2371.92399
2.42-2.487.50.20852610.9820.080.2231.94499.2
2.48-2.547.60.18352990.9860.070.1971.99799.3
2.54-2.617.60.17153110.9860.0650.1842.08299.4
2.61-2.697.60.16253120.9890.0620.1742.04799.6
2.69-2.777.70.14953330.990.0570.162.09799.4
2.77-2.877.80.13453370.9910.0510.1442.17299.6
2.87-2.997.80.12153530.9920.0460.132.23299.7
2.99-3.127.80.10853400.9930.0410.1152.29699.6
3.12-3.297.80.09453860.9950.0350.12.43399.8
3.29-3.4980.08653690.9950.0320.0922.6799.8
3.49-3.7680.07853990.9950.0290.0832.93499.9
3.76-4.148.10.0754360.9960.0260.0743.04499.9
4.14-4.7480.06654500.9960.0250.0713.264100
4.74-5.977.90.06955040.9960.0260.0733.086100
5.97-507.40.06956820.9940.0270.0743.65899.1

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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: 2.2→32.07 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.93 / SU B: 4.149 / SU ML: 0.106 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.18 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2059 5285 4.9 %RANDOM
Rwork0.1635 ---
obs0.1655 101608 99.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 98.51 Å2 / Biso mean: 22.616 Å2 / Biso min: 6.83 Å2
Baniso -1Baniso -2Baniso -3
1--2.02 Å2-0 Å2-0 Å2
2---1.73 Å20 Å2
3---3.75 Å2
Refinement stepCycle: final / Resolution: 2.2→32.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11770 0 24 678 12472
Biso mean--39.6 26.03 -
Num. residues----1602
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01311957
X-RAY DIFFRACTIONr_bond_other_d0.0010.01511707
X-RAY DIFFRACTIONr_angle_refined_deg1.6521.63516181
X-RAY DIFFRACTIONr_angle_other_deg1.3921.57926821
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.23651595
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.07420.684629
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.411151947
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.87115125
X-RAY DIFFRACTIONr_chiral_restr0.0830.21550
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213850
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022692
LS refinement shellResolution: 2.201→2.258 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.237 361 -
Rwork0.18 7185 -
all-7546 -
obs--95.65 %

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