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- PDB-7o1g: Structure of Mycobacterium tuberculosis beta-oxidation trifunctio... -

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Basic information

Entry
Database: PDB / ID: 7o1g
TitleStructure of Mycobacterium tuberculosis beta-oxidation trifunctional enzyme alpha-E141A-H462A, 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: 3.03 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 / diffrn_source / pdbx_database_proc / pdbx_struct_ref_seq_depositor_info
Item: _citation.journal_volume / _citation_author.name ..._citation.journal_volume / _citation_author.name / _diffrn_source.pdbx_synchrotron_site / _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 ...chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model
Item: _diffrn_source.pdbx_synchrotron_site

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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)120,7897
Polymers120,3092
Non-polymers4805
Water1629
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)241,57914
Polymers240,6184
Non-polymers96110
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area13040 Å2
ΔGint-142 kcal/mol
Surface area82780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.610, 207.800, 132.990
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: 42428.289 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: 77880.703 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-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.9 Å3/Da / Density % sol: 58 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 5.5 / Details: 2 M Ammonium Sulfate, 0.1M MES pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.03→51.95 Å / Num. obs: 27721 / % possible obs: 99.9 % / Redundancy: 6.4 % / Biso Wilson estimate: 83.87 Å2 / CC1/2: 0.987 / Net I/σ(I): 6.8
Reflection shellResolution: 3.03→3.08 Å / Num. unique obs: 4415 / CC1/2: 0.52

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Processing

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

4b3h


Resolution: 3.03→51.95 Å / SU ML: 0.5702 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.1529
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2752 1372 4.96 %
Rwork0.2256 26298 -
obs0.2282 27670 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 97.38 Å2
Refinement stepCycle: LAST / Resolution: 3.03→51.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8334 0 25 9 8368
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00168511
X-RAY DIFFRACTIONf_angle_d0.414511536
X-RAY DIFFRACTIONf_chiral_restr0.03881316
X-RAY DIFFRACTIONf_plane_restr0.00361518
X-RAY DIFFRACTIONf_dihedral_angle_d11.64613116
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.03-3.140.42441430.37282567X-RAY DIFFRACTION99.74
3.14-3.260.41761160.35982616X-RAY DIFFRACTION99.56
3.26-3.410.39891510.35522592X-RAY DIFFRACTION99.67
3.41-3.590.47021410.36192580X-RAY DIFFRACTION99.74
3.59-3.820.32961250.27532622X-RAY DIFFRACTION99.85
3.82-4.110.26311240.20822630X-RAY DIFFRACTION99.82
4.11-4.530.23011330.17422634X-RAY DIFFRACTION99.96
4.53-5.180.2091410.17122646X-RAY DIFFRACTION99.93
5.18-6.520.26721440.21232660X-RAY DIFFRACTION99.96
6.53-51.950.21721540.18132751X-RAY DIFFRACTION99.38
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.35649159161-0.190904363847-0.05453587651822.311902768670.09703855314121.875889690270.05258519773820.16349072320.0817654183043-0.2038888321280.02414779144520.138198244034-0.05106571625430.230066874896-0.0674927462660.622249331791-0.009131387576090.04279314188950.629880276069-0.01303407277940.466907421071-14.0954824881-0.470093379279-16.1633087363
20.551844815968-0.0181316615989-0.05767029143581.01513760836-0.5383835493960.855833220689-0.09774604470460.1315518974140.309296573368-0.2810957960710.001718465973710.0966206272978-0.407375862064-0.03109668547410.0730107776341.118437782980.0199096031318-0.05791862238940.67764504690.02139886251530.822489798097-42.792083896642.1219722929-4.40565290113
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain D and resseq 2:403)DA2 - 4031 - 406
22(chain A and resseq -13:720)AB-13 - 7201 - 729

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