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- PDB-8gql: X-ray structure of Thiolase from Pseudomonas aeruginosa PAO1 -

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Basic information

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


small molecule metabolic process / acetyl-CoA C-acetyltransferase activity
Similarity search - Function
Thiolase, active site / Thiolases active site. / 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
Probable acyl-CoA thiolase
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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)166,7715
Polymers166,6794
Non-polymers921
Water5,783321
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14030 Å2
ΔGint-53 kcal/mol
Surface area47860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.098, 93.751, 111.526
Angle α, β, γ (deg.)90.000, 108.290, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Thiolase


Mass: 41669.664 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: PA3925 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G3XD40
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 321 / 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: 2.21 Å3/Da / Density % sol: 44.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 16% (w/v) PEG 3350 200 mM Magnesium acetate tetrahydrate

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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: Dec 1, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 63474 / % possible obs: 98.4 % / Redundancy: 3 % / Rmerge(I) obs: 0.179 / Rpim(I) all: 0.119 / Rrim(I) all: 0.215 / Χ2: 9.278 / Net I/σ(I): 9.5 / Num. measured all: 190736
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.3-2.3430.43231660.7290.2880.5213.75198.5
2.34-2.3830.39631610.7590.2630.4773.99898.5
2.38-2.4330.38431470.7510.2570.4634.11698.5
2.43-2.4830.38431560.7590.2560.4634.91198.7
2.48-2.5330.3631890.7830.2410.4354.74198.8
2.53-2.5930.34231340.7770.2290.4145.43397.9
2.59-2.6630.31431890.8290.2110.386.27898.4
2.66-2.7330.331610.810.2030.3646.04998.8
2.73-2.8130.26631440.8530.1790.3226.898.3
2.81-2.930.2531560.8630.1680.3037.38898.7
2.9-330.23331960.8870.1550.2817.59798.4
3-3.122.90.22331770.8890.150.279.05898.5
3.12-3.2630.20831690.8830.1390.25111.43298.6
3.26-3.4430.18731680.8750.1250.22612.67898.6
3.44-3.6530.17332050.9090.1150.20914.85698.7
3.65-3.9330.16431600.8810.1110.19918.70398
3.93-4.332.90.14431770.9160.0970.17519.76797.8
4.33-4.952.90.13531590.9280.0910.16418.6197.2
4.95-6.243.20.12632410.9320.0810.15111.09299.4
6.24-503.10.09432190.9730.0610.1139.38996.8

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4N44

4n44


Resolution: 2.3→34.47 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.88 / SU B: 8.67 / SU ML: 0.209 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.403 / ESU R Free: 0.272 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2651 3092 4.9 %RANDOM
Rwork0.1908 ---
obs0.1944 60362 97.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 91.91 Å2 / Biso mean: 28.917 Å2 / Biso min: 11.42 Å2
Baniso -1Baniso -2Baniso -3
1-1.84 Å20 Å20.46 Å2
2---2.3 Å2-0 Å2
3---0.13 Å2
Refinement stepCycle: final / Resolution: 2.3→34.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11196 0 6 321 11523
Biso mean--34.37 27.9 -
Num. residues----1549
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01311330
X-RAY DIFFRACTIONr_bond_other_d0.0010.01511154
X-RAY DIFFRACTIONr_angle_refined_deg1.7471.63115293
X-RAY DIFFRACTIONr_angle_other_deg1.3221.57825635
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.09251542
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.39921.952502
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.068151938
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7911581
X-RAY DIFFRACTIONr_chiral_restr0.0780.21539
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213035
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022383
LS refinement shellResolution: 2.3→2.355 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.297 202 -
Rwork0.213 4164 -
obs--92.23 %

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