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- PDB-8oql: Structure of Mycobacterium tuberculosis beta-oxidation trifunctio... -

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Basic information

Entry
Database: PDB / ID: 8oql
TitleStructure of Mycobacterium tuberculosis beta-oxidation trifunctional enzyme in complex with Fragment-M-1
Components
  • 3-hydroxyacyl-CoA dehydrogenase
  • Putative acyltransferase Rv0859
KeywordsOXIDOREDUCTASE / fatty acid beta oxidation complex / mycobacterium tuberculosis / TFE / fragment screening / substrate channeling
Function / homology
Function and homology information


long-chain-3-hydroxyacyl-CoA dehydrogenase activity / enoyl-CoA hydratase activity / fatty acid beta-oxidation / acyltransferase activity, transferring groups other than amino-acyl groups / NAD+ binding / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / peptidoglycan-based cell wall / plasma membrane / cytosol
Similarity search - Function
3-hydroxyacyl-CoA dehydrogenase, C-terminal / 3-hydroxyacyl-CoA dehydrogenase, NAD binding / 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain / 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain / Thiolase, active site / Thiolases active site. / Thiolase, acyl-enzyme intermediate active site / Thiolases acyl-enzyme intermediate signature. / Thiolase, conserved site / Thiolases signature 2. ...3-hydroxyacyl-CoA dehydrogenase, C-terminal / 3-hydroxyacyl-CoA dehydrogenase, NAD binding / 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain / 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain / Thiolase, active site / Thiolases active site. / Thiolase, acyl-enzyme intermediate active site / Thiolases acyl-enzyme intermediate signature. / Thiolase, conserved site / Thiolases signature 2. / Thiolase / Thiolase, C-terminal / Thiolase, C-terminal domain / Thiolase, N-terminal / Thiolase, N-terminal domain / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / ClpP/crotonase-like domain superfamily / Thiolase-like / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Hexafluorophosphate anion / FORMAMIDE / Putative acyltransferase Rv0859 / Probable fatty oxidation protein FadB
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsDalwani, S. / Wierenga, R.K. / Venkatesan, R.
Funding support Finland, 3items
OrganizationGrant numberCountry
Academy of Finland293369 Finland
Academy of Finland289024 Finland
Academy of Finland319194 Finland
Citation
Journal: Biorxiv / Year: 2024
Title: Crystallographic fragment binding studies of the Mycobacterium tuberculosis trifunctional enzyme suggest binding pockets for the tails of the acyl-CoA substrates at its active sites and a ...Title: Crystallographic fragment binding studies of the Mycobacterium tuberculosis trifunctional enzyme suggest binding pockets for the tails of the acyl-CoA substrates at its active sites and a potential substrate channeling path between them
Authors: Dalwani, S. / Metz, A. / Huschmann, F.U. / Weiss, M.S. / Wierenga, R.K. / Venkatesan, R.
#1: Journal: J Struct Biol / Year: 2021
Title: Substrate specificity and conformational flexibility properties of the Mycobacterium tuberculosis beta-oxidation trifunctional enzyme.
Authors: Dalwani, S.
#2: Journal: ACS Chem Biol / Year: 2013
Title: Structure of mycobacterial beta-oxidation trifunctional enzyme reveals its altered assembly and putative substrate channeling pathway.
Authors: Venkatesan, R. / Wierenga, R.K.
History
DepositionApr 12, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 24, 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: 3-hydroxyacyl-CoA dehydrogenase
B: 3-hydroxyacyl-CoA dehydrogenase
C: Putative acyltransferase Rv0859
D: Putative acyltransferase Rv0859
hetero molecules


Theoretical massNumber of molelcules
Total (without water)248,49373
Polymers240,9644
Non-polymers7,52969
Water1,38777
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18810 Å2
ΔGint-391 kcal/mol
Surface area82950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)249.623, 134.676, 119.124
Angle α, β, γ (deg.)90.000, 110.608, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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Protein , 2 types, 4 molecules ABCD

#1: Protein 3-hydroxyacyl-CoA dehydrogenase /


Mass: 78005.805 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: fadB, Rv0860 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: O53872, 3-hydroxyacyl-CoA dehydrogenase
#2: Protein Putative acyltransferase Rv0859


Mass: 42476.355 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: fadA, Rv0859 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: O53871, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups

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Non-polymers , 5 types, 146 molecules

#3: Chemical...
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 34 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-ARF / FORMAMIDE / Formamide


Type: L-peptide NH3 amino terminus / Mass: 45.041 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CH3NO
#6: Chemical...
ChemComp-A9J / Hexafluorophosphate anion


Mass: 144.964 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: F6P / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.89 Å3/Da / Density % sol: 68.37 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 2 M Ammonium Sulfate, 0.1M Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.968619 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.968619 Å / Relative weight: 1
ReflectionResolution: 2.7→48.32 Å / Num. obs: 100954 / % possible obs: 99.7 % / Redundancy: 4.8 % / Biso Wilson estimate: 71.56 Å2 / CC1/2: 0.998 / Net I/σ(I): 10.9
Reflection shellResolution: 2.7→2.75 Å / Mean I/σ(I) obs: 1.3 / Num. unique obs: 4803 / CC1/2: 0.538

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→48.32 Å / SU ML: 0.3726 / Cross valid method: FREE R-VALUE / σ(F): 0.87 / Phase error: 24.2557
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2183 4964 4.92 %
Rwork0.1824 95972 -
obs0.1842 100936 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 74.02 Å2
Refinement stepCycle: LAST / Resolution: 2.7→48.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16667 0 387 77 17131
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00217318
X-RAY DIFFRACTIONf_angle_d0.46523641
X-RAY DIFFRACTIONf_chiral_restr0.0412628
X-RAY DIFFRACTIONf_plane_restr0.00423040
X-RAY DIFFRACTIONf_dihedral_angle_d12.25146253
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.730.41421460.35383003X-RAY DIFFRACTION93.86
2.73-2.760.35351570.32793247X-RAY DIFFRACTION99.97
2.76-2.80.31081510.29643163X-RAY DIFFRACTION99.97
2.8-2.830.28861580.27453190X-RAY DIFFRACTION99.97
2.83-2.870.33171470.28013224X-RAY DIFFRACTION100
2.87-2.910.32561660.27123226X-RAY DIFFRACTION99.97
2.91-2.950.32431650.25593186X-RAY DIFFRACTION99.97
2.95-2.990.27641520.2633187X-RAY DIFFRACTION100
2.99-3.040.30971590.26213205X-RAY DIFFRACTION99.97
3.04-3.090.32651680.27093196X-RAY DIFFRACTION99.97
3.09-3.140.33431440.27483238X-RAY DIFFRACTION100
3.14-3.20.28531570.25463193X-RAY DIFFRACTION99.97
3.2-3.260.27161620.23293190X-RAY DIFFRACTION100
3.26-3.330.2671750.22253179X-RAY DIFFRACTION99.91
3.33-3.40.26291590.2143237X-RAY DIFFRACTION99.97
3.4-3.480.24711630.2113173X-RAY DIFFRACTION99.94
3.48-3.570.25871530.20163213X-RAY DIFFRACTION99.85
3.57-3.660.25271640.19243223X-RAY DIFFRACTION99.88
3.66-3.770.23591830.18833184X-RAY DIFFRACTION100
3.77-3.890.21311740.16793193X-RAY DIFFRACTION99.94
3.89-4.030.18441970.15223168X-RAY DIFFRACTION99.91
4.03-4.190.19461600.13793203X-RAY DIFFRACTION99.82
4.19-4.380.17591630.13583235X-RAY DIFFRACTION99.79
4.38-4.620.15271780.13643166X-RAY DIFFRACTION99.76
4.62-4.90.17321670.13583225X-RAY DIFFRACTION99.88
4.9-5.280.18141950.14293198X-RAY DIFFRACTION99.91
5.28-5.810.18261820.16643191X-RAY DIFFRACTION99.82
5.81-6.650.21811660.17493238X-RAY DIFFRACTION99.77
6.65-8.370.19641750.15233232X-RAY DIFFRACTION99.74
8.38-48.320.1791780.16083266X-RAY DIFFRACTION99.02
Refinement TLS params.Method: refined / Origin x: -43.8407768051 Å / Origin y: 34.1416952805 Å / Origin z: -1.64715510787 Å
111213212223313233
T0.480070552465 Å2-0.000213159278024 Å2-0.0129795520984 Å2-0.439695382513 Å20.0225302711329 Å2--0.551558561925 Å2
L0.247244022349 °20.0362000274727 °20.0189034835726 °2-0.169165880363 °2-0.00103126726513 °2--0.574746674625 °2
S-0.012696748756 Å °0.00274898206468 Å °-0.0477029770774 Å °-0.0187804608054 Å °-0.00274974057296 Å °0.0575758402027 Å °0.00624217023573 Å °-0.0757940245107 Å °0.0190561174193 Å °
Refinement TLS groupSelection details: all

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