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- PDB-7o4t: Structure of Mycobacterium tuberculosis beta-oxidation trifunctio... -

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Basic information

Entry
Database: PDB / ID: 7o4t
TitleStructure of Mycobacterium tuberculosis beta-oxidation trifunctional enzyme with Coenzyme A bound at the hydratase, thiolase active sites and possible additional binding site (CoA(ECH/HAD))
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 / 3'-PHOSPHATE-ADENOSINE-5'-DIPHOSPHATE / 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: 2.1 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)249,42242
Polymers240,9324
Non-polymers8,49038
Water4,774265
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22790 Å2
ΔGint-296 kcal/mol
Surface area83370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)247.539, 136.253, 117.799
Angle α, β, γ (deg.)90.000, 110.496, 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-606-

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 , 5 types, 303 molecules

#3: Chemical
ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PAP / 3'-PHOSPHATE-ADENOSINE-5'-DIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3
#6: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 265 / 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: 68.29 %
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: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.1→58.74 Å / Num. obs: 212119 / % possible obs: 99.7 % / Redundancy: 5.1 % / Biso Wilson estimate: 51.73 Å2 / CC1/2: 0.998 / Net I/σ(I): 8.9
Reflection shellResolution: 2.1→2.14 Å / Num. unique obs: 10533 / CC1/2: 0.41

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Processing

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

4b3h


Resolution: 2.1→58.74 Å / SU ML: 0.3477 / Cross valid method: FREE R-VALUE / σ(F): 0.69 / Phase error: 31.0567
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2337 10659 5.03 %
Rwork0.2058 201354 -
obs0.2072 212013 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 66.84 Å2
Refinement stepCycle: LAST / Resolution: 2.1→58.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16749 0 503 265 17517
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001817578
X-RAY DIFFRACTIONf_angle_d0.545123885
X-RAY DIFFRACTIONf_chiral_restr0.04212686
X-RAY DIFFRACTIONf_plane_restr0.00373085
X-RAY DIFFRACTIONf_dihedral_angle_d13.08726518
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.120.46143680.43196654X-RAY DIFFRACTION99.57
2.12-2.150.42773440.40756701X-RAY DIFFRACTION99.48
2.15-2.180.39953320.39136719X-RAY DIFFRACTION99.62
2.18-2.20.39953620.37976683X-RAY DIFFRACTION99.7
2.2-2.230.36993540.3636738X-RAY DIFFRACTION99.72
2.23-2.260.38833620.35336640X-RAY DIFFRACTION99.38
2.26-2.290.33633250.32326704X-RAY DIFFRACTION99.29
2.29-2.330.35723440.31226654X-RAY DIFFRACTION99.42
2.33-2.370.30053420.30336731X-RAY DIFFRACTION99.55
2.37-2.40.31333450.28156693X-RAY DIFFRACTION99.56
2.4-2.450.33053930.26296647X-RAY DIFFRACTION99.59
2.45-2.490.28483760.27026658X-RAY DIFFRACTION99.56
2.49-2.540.29773790.25746654X-RAY DIFFRACTION99.43
2.54-2.590.30643430.25176707X-RAY DIFFRACTION99.59
2.59-2.650.28943670.24786711X-RAY DIFFRACTION99.83
2.65-2.710.29983740.24656698X-RAY DIFFRACTION99.92
2.71-2.770.2883590.24766733X-RAY DIFFRACTION99.94
2.78-2.850.27713570.2556720X-RAY DIFFRACTION99.89
2.85-2.930.27973760.24816684X-RAY DIFFRACTION99.79
2.93-3.030.29913550.25796737X-RAY DIFFRACTION99.83
3.03-3.140.32723690.25826718X-RAY DIFFRACTION99.73
3.14-3.260.26793670.23626731X-RAY DIFFRACTION99.87
3.26-3.410.24463200.22366747X-RAY DIFFRACTION99.79
3.41-3.590.22873440.20576728X-RAY DIFFRACTION99.83
3.59-3.820.20913710.18416753X-RAY DIFFRACTION99.66
3.82-4.110.17853240.1596730X-RAY DIFFRACTION99.41
4.11-4.520.15583530.14266727X-RAY DIFFRACTION99.1
4.52-5.180.18373350.14566740X-RAY DIFFRACTION99.44
5.18-6.520.19453650.16856767X-RAY DIFFRACTION99.6
6.52-58.740.17243540.15856847X-RAY DIFFRACTION98.96

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