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- PDB-7o1j: Structure of Mycobacterium tuberculosis beta-oxidation trifunctio... -

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Basic information

Entry
Database: PDB / ID: 7o1j
TitleStructure of Mycobacterium tuberculosis beta-oxidation trifunctional enzyme beta-C92A mutant
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
Putative acyltransferase Rv0859 / Probable fatty oxidation protein FadB
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.36 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
DepositionMar 29, 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
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: Putative acyltransferase Rv0859
A: 3-hydroxyacyl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,97518
Polymers120,4502
Non-polymers1,52516
Water2,576143
1
D: Putative acyltransferase Rv0859
A: 3-hydroxyacyl-CoA dehydrogenase
hetero molecules

D: Putative acyltransferase Rv0859
A: 3-hydroxyacyl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)243,95036
Polymers240,9004
Non-polymers3,05032
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area16770 Å2
ΔGint-317 kcal/mol
Surface area80690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.329, 209.277, 133.454
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Putative acyltransferase Rv0859


Mass: 42444.289 Da / Num. of mol.: 1
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
#2: Protein 3-hydroxyacyl-CoA dehydrogenase


Mass: 78005.805 Da / Num. of mol.: 1
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
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.94 Å3/Da / Density % sol: 58.3 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 7.5 / Details: 2 M Ammonium Sulfate, 0.1M Tea pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 2.36→66.73 Å / Num. obs: 58404 / % possible obs: 99.7 % / Redundancy: 4.3 % / Biso Wilson estimate: 45.43 Å2 / CC1/2: 0.996 / Net I/σ(I): 8
Reflection shellResolution: 2.36→2.42 Å / Num. unique obs: 4525 / CC1/2: 0.588 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
xia2data reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4B3H

4b3h


Resolution: 2.36→66.73 Å / SU ML: 0.3161 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.9623
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2496 2821 4.85 %
Rwork0.211 55401 -
obs0.2129 58222 99.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 66.91 Å2
Refinement stepCycle: LAST / Resolution: 2.36→66.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8160 0 83 143 8386
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0028385
X-RAY DIFFRACTIONf_angle_d0.490511389
X-RAY DIFFRACTIONf_chiral_restr0.04061306
X-RAY DIFFRACTIONf_plane_restr0.00371494
X-RAY DIFFRACTIONf_dihedral_angle_d12.8133002
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.36-2.40.38571230.33992713X-RAY DIFFRACTION99.16
2.4-2.440.32471450.32852727X-RAY DIFFRACTION99.48
2.44-2.490.34751570.31012726X-RAY DIFFRACTION99.28
2.49-2.540.29191260.30172753X-RAY DIFFRACTION99.45
2.54-2.60.32271360.2922759X-RAY DIFFRACTION99.48
2.6-2.660.35741270.26892764X-RAY DIFFRACTION99.69
2.66-2.720.29411540.26762688X-RAY DIFFRACTION97.76
2.72-2.80.28921290.26182752X-RAY DIFFRACTION98.97
2.8-2.880.32031400.25532751X-RAY DIFFRACTION99.93
2.88-2.970.28861270.25692793X-RAY DIFFRACTION99.83
2.97-3.080.30051510.25432759X-RAY DIFFRACTION99.97
3.08-3.20.30341480.24642745X-RAY DIFFRACTION99.86
3.2-3.350.2931560.23522789X-RAY DIFFRACTION99.9
3.35-3.530.28221430.21552762X-RAY DIFFRACTION99.86
3.53-3.750.29261370.25052742X-RAY DIFFRACTION98.19
3.75-4.040.18711480.1742765X-RAY DIFFRACTION98.85
4.04-4.440.20441300.15192802X-RAY DIFFRACTION99.56
4.44-5.080.19151510.15562824X-RAY DIFFRACTION100
5.08-6.40.24181450.18272838X-RAY DIFFRACTION99.9
6.4-66.730.17161480.16312949X-RAY DIFFRACTION99.45
Refinement TLS params.Method: refined / Origin x: -31.8304317201 Å / Origin y: 26.0505947014 Å / Origin z: -8.54851237867 Å
111213212223313233
T0.480395670512 Å2-0.00555700619692 Å2-0.012819630609 Å2-0.387422767274 Å20.0618177633745 Å2--0.30984465875 Å2
L0.431402295964 °2-0.0445128428749 °20.0304296277481 °2-0.778235352619 °20.0536560939201 °2--0.587478480138 °2
S0.024975186647 Å °0.0756994692052 Å °0.189504667785 Å °-0.21513934492 Å °-2.77641883664E-6 Å °0.0325249362774 Å °-0.343843044621 Å °0.0214766657108 Å °-0.0240340460208 Å °
Refinement TLS groupSelection details: all

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