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- PDB-7o4r: Structure of Mycobacterium tuberculosis beta-oxidation trifunctio... -

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Basic information

Entry
Database: PDB / ID: 7o4r
TitleStructure of Mycobacterium tuberculosis beta-oxidation trifunctional enzyme with Coenzyme A bound at the thiolase active sites and additional binding site (CoA(HAD/KAT))
Components
  • 3-hydroxyacyl-CoA dehydrogenase
  • Putative acyltransferase Rv0859
KeywordsOXIDOREDUCTASE / trifunctional enzyme / fatty acid beta oxidation / mycobacterium tuberculosis
Function / homology
Function and homology information


long-chain (3S)-3-hydroxyacyl-CoA dehydrogenase (NAD+) activity / acetyl-CoA C-acetyltransferase activity / enoyl-CoA hydratase activity / 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, conserved site / Thiolases signature 2. / Thiolase, acyl-enzyme intermediate active site ...: / 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, 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 / 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
COENZYME A / Putative acyltransferase Rv0859 / Probable fatty oxidation protein FadB
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
Mycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.79 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: J.Struct.Biol. / Year: 2021
Title: Substrate specificity and conformational flexibility properties of the Mycobacterium tuberculosis beta-oxidation trifunctional enzyme.
Authors: Dalwani, S. / Lampela, O. / Leprovost, P. / Schmitz, W. / Juffer, A.H. / Wierenga, R.K. / Venkatesan, R.
#1: 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 7, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 25, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 22, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / pdbx_database_proc / pdbx_struct_ref_seq_depositor_info
Item: _citation.journal_volume / _citation_author.name / _pdbx_struct_ref_seq_depositor_info.db_seq_one_letter_code
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)246,49634
Polymers240,9324
Non-polymers5,56430
Water4,125229
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19450 Å2
ΔGint-300 kcal/mol
Surface area83390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)248.254, 135.752, 119.304
Angle α, β, γ (deg.)90.000, 110.514, 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
Components on special symmetry positions
IDModelComponents
11C-609-

HOH

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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 (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / 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, 259 molecules

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


Mass: 96.063 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / 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: 3.93 Å3/Da / Density % sol: 68.68 %
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: ESRF / Beamline: ID29 / Wavelength: 1.0722 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0722 Å / Relative weight: 1
ReflectionResolution: 2.79→48.5 Å / Num. obs: 81071 / % possible obs: 95.1 % / Redundancy: 3.4 % / Biso Wilson estimate: 50.68 Å2 / CC1/2: 0.995 / Net I/σ(I): 10.5
Reflection shellResolution: 2.79→2.9 Å / Num. unique obs: 4054 / CC1/2: 0.473

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4B3H

4b3h


Resolution: 2.79→48.5 Å / SU ML: 0.3365 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 22.8104
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2157 4034 5.04 %
Rwork0.1782 76044 -
obs0.1802 80078 86.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.83 Å2
Refinement stepCycle: LAST / Resolution: 2.79→48.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16674 0 323 229 17226
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001417275
X-RAY DIFFRACTIONf_angle_d0.415723436
X-RAY DIFFRACTIONf_chiral_restr0.03922645
X-RAY DIFFRACTIONf_plane_restr0.00353049
X-RAY DIFFRACTIONf_dihedral_angle_d11.57446361
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.79-2.820.4686480.4077815X-RAY DIFFRACTION26.91
2.82-2.860.3907510.32821109X-RAY DIFFRACTION36.87
2.86-2.890.3189720.321302X-RAY DIFFRACTION43.41
2.89-2.930.3292690.30541384X-RAY DIFFRACTION46.41
2.93-2.970.3693990.30351648X-RAY DIFFRACTION54.59
2.97-3.010.33831100.28482011X-RAY DIFFRACTION66.8
3.01-3.060.35081060.28122246X-RAY DIFFRACTION74.64
3.06-3.110.33231260.26962550X-RAY DIFFRACTION85.01
3.11-3.160.33531320.25282850X-RAY DIFFRACTION93.36
3.16-3.210.29031550.24482929X-RAY DIFFRACTION97.69
3.21-3.270.331560.23252972X-RAY DIFFRACTION99.71
3.27-3.330.29371710.2292993X-RAY DIFFRACTION99.84
3.33-3.40.29331660.22053026X-RAY DIFFRACTION99.81
3.4-3.470.25091510.20343027X-RAY DIFFRACTION99.87
3.47-3.560.23531370.20263011X-RAY DIFFRACTION99.81
3.56-3.640.23681500.17843000X-RAY DIFFRACTION99.68
3.64-3.740.21561620.17033009X-RAY DIFFRACTION99.34
3.74-3.850.19821630.16153019X-RAY DIFFRACTION99.34
3.85-3.980.20441540.14662972X-RAY DIFFRACTION98.67
3.98-4.120.19081680.14112994X-RAY DIFFRACTION99.75
4.12-4.280.16881710.13512997X-RAY DIFFRACTION99.53
4.28-4.480.1721660.13142989X-RAY DIFFRACTION99.62
4.48-4.720.15111610.12893021X-RAY DIFFRACTION99.69
4.72-5.010.1641610.13793018X-RAY DIFFRACTION99.62
5.01-5.40.1841640.14553014X-RAY DIFFRACTION99.5
5.4-5.940.19431830.17282981X-RAY DIFFRACTION99
5.94-6.80.20751610.16913039X-RAY DIFFRACTION99.78
6.8-8.550.16181620.15393038X-RAY DIFFRACTION99.32
8.56-48.50.17021590.16243080X-RAY DIFFRACTION98.99

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