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- PDB-8gqm: Crystal structure of Thiolase complexed with acetyl coenzyme A -

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Basic information

Entry
Database: PDB / ID: 8gqm
TitleCrystal structure of Thiolase complexed with acetyl coenzyme A
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, 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
ACETYL COENZYME *A / Probable acyl-CoA thiolase
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 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

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Assembly

Deposited unit
A: Thiolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3773
Polymers42,4751
Non-polymers9022
Water6,846380
1
A: Thiolase
hetero molecules

A: Thiolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,7546
Polymers84,9512
Non-polymers1,8034
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area5880 Å2
ΔGint-29 kcal/mol
Surface area25830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.986, 90.970, 98.706
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Thiolase


Mass: 42475.488 Da / Num. of mol.: 1
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: PA2940 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9HZQ7
#2: Chemical ChemComp-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 380 / 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: 2.17 Å3/Da / Density % sol: 43.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 20% (v/v) 1,4-butanediol 100 mM Sodium acetate, pH 5.5 15mM Acetyl-CoA

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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 4, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. obs: 65560 / % possible obs: 99.9 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.029 / Rrim(I) all: 0.078 / Χ2: 1.449 / Net I/σ(I): 8.5 / Num. measured all: 475648
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.45-1.487.20.47632580.9190.190.5141.094100
1.48-1.57.30.4832270.9250.1910.5171.111100
1.5-1.537.30.42232670.9370.1680.4551.179100
1.53-1.567.30.35932360.9560.1430.3871.212100
1.56-1.67.30.31932230.9620.1270.3441.252100
1.6-1.637.30.28432560.9660.1130.3071.312100
1.63-1.677.30.24332490.970.0970.2631.374100
1.67-1.727.40.21832600.9770.0870.2351.394100
1.72-1.777.40.18632680.9850.0740.21.421100
1.77-1.837.40.15932600.9840.0640.1721.513100
1.83-1.897.30.14132540.9880.0560.1521.494100
1.89-1.977.30.12432770.9910.0490.1331.844100
1.97-2.067.30.0932610.9960.0360.0971.469100
2.06-2.177.30.07632720.9970.030.0821.43899.9
2.17-2.37.30.07832800.9960.0310.0842.141100
2.3-2.487.30.05932890.9980.0230.0631.459100
2.48-2.737.30.05133040.9980.020.0551.40599.9
2.73-3.127.20.04333200.9980.0170.0461.373100
3.12-3.9470.0433250.9990.0160.0431.72199.4
3.94-506.70.04134740.9980.0170.0441.78999.6

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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: 1.45→28.96 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.963 / SU B: 0.956 / SU ML: 0.037 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.057 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.176 3186 4.9 %RANDOM
Rwork0.1525 ---
obs0.1537 62310 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 58.26 Å2 / Biso mean: 13.912 Å2 / Biso min: 6.06 Å2
Baniso -1Baniso -2Baniso -3
1--0.77 Å2-0 Å2-0 Å2
2--1.36 Å2-0 Å2
3----0.59 Å2
Refinement stepCycle: final / Resolution: 1.45→28.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2730 0 57 383 3170
Biso mean--25.27 27.2 -
Num. residues----377
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0132841
X-RAY DIFFRACTIONr_bond_other_d0.0010.0152779
X-RAY DIFFRACTIONr_angle_refined_deg1.8891.6353856
X-RAY DIFFRACTIONr_angle_other_deg1.6131.5716366
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6535380
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.16920.37135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.15815450
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0111526
X-RAY DIFFRACTIONr_chiral_restr0.0970.2381
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023268
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02627
LS refinement shellResolution: 1.45→1.486 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.236 228 -
Rwork0.203 4476 -
obs--97.67 %

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