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

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Basic information

Entry
Database: PDB / ID: 8opw
TitleStructure of Mycobacterium tuberculosis beta-oxidation trifunctional enzyme in complex with Caffeine (Fragment-B-51)
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 / acyltransferase activity, transferring groups other than amino-acyl groups / fatty acid beta-oxidation / 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
CAFFEINE / Putative acyltransferase Rv0859 / Probable fatty oxidation protein FadB
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.52 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: Wierenga, R.K.
History
DepositionApr 10, 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)244,46339
Polymers240,9324
Non-polymers3,53135
Water3,279182
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18170 Å2
ΔGint-307 kcal/mol
Surface area83140 Å2
Unit cell
Length a, b, c (Å)249.512, 134.500, 118.978
Angle α, β, γ (deg.)90.000, 110.861, 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: 42460.355 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 , 4 types, 217 molecules

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


Mass: 96.063 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CFF / CAFFEINE / 3,7-DIHYDRO-1,3,7-TRIMETHYL-1H-PURINE-2,6-DIONE


Mass: 194.191 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10N4O2 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / 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: 3.87 Å3/Da / Density % sol: 68.23 %
Crystal growTemperature: 295 K / Method: vapor diffusion / 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: BESSY / Beamline: 14.1 / Wavelength: 0.895 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.895 Å / Relative weight: 1
ReflectionResolution: 2.51→48.19 Å / Num. obs: 121668 / % possible obs: 97.5 % / Redundancy: 3.8 % / Biso Wilson estimate: 57.25 Å2 / CC1/2: 0.99 / Net I/σ(I): 6
Reflection shellResolution: 2.51→2.67 Å / Num. unique obs: 17971 / CC1/2: 0.144

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.52→48.19 Å / SU ML: 0.452 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.8731
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2398 2074 1.72 %
Rwork0.2084 118584 -
obs0.209 120658 96.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 66.17 Å2
Refinement stepCycle: LAST / Resolution: 2.52→48.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16688 0 200 182 17070
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001817188
X-RAY DIFFRACTIONf_angle_d0.451923288
X-RAY DIFFRACTIONf_chiral_restr0.04012626
X-RAY DIFFRACTIONf_plane_restr0.0043043
X-RAY DIFFRACTIONf_dihedral_angle_d11.72926279
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.52-2.570.4071990.40625903X-RAY DIFFRACTION72.35
2.57-2.640.40131310.37447576X-RAY DIFFRACTION92.88
2.64-2.710.38681400.34948047X-RAY DIFFRACTION99.3
2.71-2.790.37251400.32928078X-RAY DIFFRACTION99.5
2.79-2.880.35181420.31768086X-RAY DIFFRACTION99.48
2.88-2.980.3231420.31238062X-RAY DIFFRACTION99.09
2.98-3.10.36721390.32617951X-RAY DIFFRACTION97.98
3.1-3.240.31311430.2758111X-RAY DIFFRACTION99.81
3.24-3.410.29171430.24198139X-RAY DIFFRACTION99.69
3.41-3.630.25931420.21378112X-RAY DIFFRACTION99.33
3.63-3.910.21561410.18368010X-RAY DIFFRACTION98.32
3.91-4.30.19521430.14858157X-RAY DIFFRACTION99.63
4.3-4.920.17431420.14148069X-RAY DIFFRACTION98.89
4.92-6.20.19391430.1638145X-RAY DIFFRACTION99.12
6.2-48.190.15791440.15118138X-RAY DIFFRACTION97.83
Refinement TLS params.Method: refined / Origin x: -43.7134162577 Å / Origin y: 34.1594605327 Å / Origin z: -1.80115113385 Å
111213212223313233
T0.369502127161 Å20.00406370286591 Å20.00371924673266 Å2-0.342869878557 Å20.0197328190952 Å2--0.42332009764 Å2
L0.218138640713 °20.0244448192097 °2-0.000662799862969 °2-0.15478055267 °20.0088965278669 °2--0.414083528487 °2
S-0.0103516987922 Å °-0.00469975304975 Å °-0.0485502628428 Å °-0.014173044657 Å °-0.00041756601193 Å °0.0256567024283 Å °0.0231151628146 Å °-0.0706256573304 Å °0.0123959101247 Å °
Refinement TLS groupSelection details: all

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