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- PDB-7o1m: Structure of Mycobacterium tuberculosis beta-oxidation trifunctio... -

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Basic information

Entry
Database: PDB / ID: 7o1m
TitleStructure of Mycobacterium tuberculosis beta-oxidation trifunctional enzyme alpha-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: 2.89 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

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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)121,13210
Polymers120,3672
Non-polymers7658
Water1448
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)242,26320
Polymers240,7344
Non-polymers1,52916
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area14400 Å2
ΔGint-189 kcal/mol
Surface area82730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.057, 212.370, 134.004
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: 77938.734 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.: 7 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 3.1 Å3/Da / Density % sol: 60.2 %
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: 2.89→46.72 Å / Num. obs: 32438 / % possible obs: 97.6 % / Redundancy: 4.2 % / Biso Wilson estimate: 92.06 Å2 / CC1/2: 0.998 / Net I/σ(I): 10.2
Reflection shellResolution: 2.89→3.07 Å / Num. unique obs: 4254 / CC1/2: 0.597

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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: 2.89→44.08 Å / SU ML: 0.491 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 33.7059
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2546 1597 4.95 %
Rwork0.2122 30676 -
obs0.2144 32273 96.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 110.9 Å2
Refinement stepCycle: LAST / Resolution: 2.89→44.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8139 0 41 8 8188
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00168318
X-RAY DIFFRACTIONf_angle_d0.422711300
X-RAY DIFFRACTIONf_chiral_restr0.03951306
X-RAY DIFFRACTIONf_plane_restr0.00381490
X-RAY DIFFRACTIONf_dihedral_angle_d12.57362975
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.89-2.990.45481360.38272709X-RAY DIFFRACTION94.68
2.99-3.090.34421620.33452842X-RAY DIFFRACTION99.7
3.09-3.220.32721410.29462841X-RAY DIFFRACTION99.47
3.22-3.360.37541210.27092860X-RAY DIFFRACTION98.74
3.36-3.540.35651320.312637X-RAY DIFFRACTION91.78
3.54-3.760.32291300.29782606X-RAY DIFFRACTION90.75
3.76-4.050.3051430.24082538X-RAY DIFFRACTION87.96
4.05-4.460.21651610.17312878X-RAY DIFFRACTION99.64
4.46-5.10.221600.16362869X-RAY DIFFRACTION99.08
5.1-6.430.23771370.19962927X-RAY DIFFRACTION99.35
6.43-44.080.20651740.1672969X-RAY DIFFRACTION97.67
Refinement TLS params.Method: refined / Origin x: -32.8745392266 Å / Origin y: 26.6654341375 Å / Origin z: -8.3933332338 Å
111213212223313233
T1.03953597958 Å20.0256848327921 Å20.0549521753967 Å2-0.687272667471 Å20.0289724213213 Å2--0.534578405942 Å2
L0.665554883979 °2-0.175573381259 °20.211383399928 °2-0.802659135952 °20.0661127662189 °2--0.417136157033 °2
S-0.00203627716404 Å °0.0560086356402 Å °0.182575614557 Å °-0.261051426123 Å °-0.0244719748823 Å °0.0616548874268 Å °-0.178089346332 Å °0.020628796487 Å °0.0263135278417 Å °
Refinement TLS groupSelection details: all

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