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- PDB-8oqv: Structure of Mycobacterium tuberculosis beta-oxidation trifunctio... -

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Basic information

Entry
Database: PDB / ID: 8oqv
TitleStructure of Mycobacterium tuberculosis beta-oxidation trifunctional enzyme in complex with Fragment-M-109
Components
  • 3-hydroxyacyl-CoA dehydrogenase
  • Putative acyltransferase Rv0859
KeywordsOXIDOREDUCTASE / fatty acid beta oxidation complex / mycobacterium tuberculosis / TFE / fragment screening / substrate channeling
Function / homology
Function and homology information


long-chain-3-hydroxyacyl-CoA dehydrogenase 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, acyl-enzyme intermediate active site / Thiolases acyl-enzyme intermediate signature. / Thiolase, conserved 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, acyl-enzyme intermediate active site / Thiolases acyl-enzyme intermediate signature. / Thiolase, conserved site / Thiolases signature 2. / 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
4-nitrobenzenesulfonic acid / Putative acyltransferase Rv0859 / Probable fatty oxidation protein FadB
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.78 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: Acta Crystallogr D Struct Biol / Year: 2024
Title: Crystallographic fragment-binding studies of the Mycobacterium tuberculosis trifunctional enzyme suggest binding pockets for the tails of the acyl-CoA substrates at its active sites and a ...Title: Crystallographic fragment-binding studies of the Mycobacterium tuberculosis trifunctional enzyme suggest binding pockets for the tails of the acyl-CoA substrates at its active sites and a potential substrate-channeling path between them.
Authors: Dalwani, S. / Metz, A. / Huschmann, F.U. / Weiss, M.S. / Wierenga, R.K. / Venkatesan, R.
#1: Journal: Biorxiv / Year: 2024
Title: Crystallographic fragment binding studies of the Mycobacterium tuberculosis trifunctional enzyme suggest binding pockets for the tails of the acyl-CoA substrates at its active sites and a ...Title: Crystallographic fragment binding studies of the Mycobacterium tuberculosis trifunctional enzyme suggest binding pockets for the tails of the acyl-CoA substrates at its active sites and a potential substrate channeling path between them
Authors: Dalwani, S. / Metz, A. / Huschmann, F.U. / Weiss, M.S. / Wierenga, R.K. / Venkatesan, R.
#2: Journal: J Struct Biol / Year: 2021
Title: Substrate specificity and conformational flexibility properties of the Mycobacterium tuberculosis beta-oxidation trifunctional enzyme.
Authors: Dalwani, S.
#3: Journal: ACS Chem Biol / Year: 2013
Title: Structure of mycobacterial beta-oxidation trifunctional enzyme reveals its altered assembly and putative substrate channeling pathway.
Authors: Wierenga, R.K.
History
DepositionApr 12, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 24, 2024Provider: repository / Type: Initial release
Revision 2.0Jul 24, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / citation / citation_author / entity / pdbx_contact_author / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / struct_asym / struct_conf / struct_mon_prot_cis / struct_sheet_range
Item: _entity.pdbx_number_of_molecules / _pdbx_poly_seq_scheme.auth_mon_id ..._entity.pdbx_number_of_molecules / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_refine_tls.L[1][1] / _pdbx_refine_tls.L[1][2] / _pdbx_refine_tls.L[1][3] / _pdbx_refine_tls.L[2][2] / _pdbx_refine_tls.L[2][3] / _pdbx_refine_tls.L[3][3] / _pdbx_refine_tls.S[1][1] / _pdbx_refine_tls.S[1][2] / _pdbx_refine_tls.S[1][3] / _pdbx_refine_tls.S[2][1] / _pdbx_refine_tls.S[2][2] / _pdbx_refine_tls.S[2][3] / _pdbx_refine_tls.S[3][1] / _pdbx_refine_tls.S[3][2] / _pdbx_refine_tls.S[3][3] / _pdbx_refine_tls.T[1][1] / _pdbx_refine_tls.T[1][2] / _pdbx_refine_tls.T[1][3] / _pdbx_refine_tls.T[2][2] / _pdbx_refine_tls.T[2][3] / _pdbx_refine_tls.T[3][3] / _pdbx_refine_tls.origin_x / _pdbx_refine_tls.origin_y / _pdbx_refine_tls.origin_z / _pdbx_refine_tls_group.end_label_asym_id / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _refine.B_iso_mean / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_number_reflns_R_work / _refine.ls_number_reflns_obs / _refine.overall_SU_ML / _refine.pdbx_overall_phase_error / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_protein / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.number_reflns_R_work / _refine_ls_shell.percent_reflns_obs / _struct_mon_prot_cis.pdbx_omega_angle / _struct_sheet_range.beg_auth_comp_id / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.beg_label_comp_id / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_auth_comp_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.end_label_comp_id / _struct_sheet_range.end_label_seq_id
Description: Model completeness
Details: Changes as suggested during the review process of article submission
Provider: author / Type: Coordinate replacement
Revision 2.1Aug 14, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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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)244,17230
Polymers240,9324
Non-polymers3,23926
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14680 Å2
ΔGint-217 kcal/mol
Surface area83020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)248.790, 135.626, 119.698
Angle α, β, γ (deg.)90.000, 110.630, 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

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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 H37Rv (bacteria)
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, 73 molecules

#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-VWI / 4-nitrobenzenesulfonic acid


Mass: 203.173 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C6H5NO5S / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 3.92 Å3/Da / Density % sol: 68.64 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / 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: MAX IV / Beamline: BioMAX / Wavelength: 0.976254 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976254 Å / Relative weight: 1
ReflectionResolution: 2.77→45.51 Å / Num. obs: 80655 / % possible obs: 91.9 % / Redundancy: 6.7 % / Biso Wilson estimate: 70.55 Å2 / CC1/2: 0.919 / Net I/σ(I): 8.3
Reflection shellResolution: 2.77→2.9 Å / Num. unique obs: 4033 / CC1/2: 0.412

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.78→45.51 Å / SU ML: 0.4058 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.68
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2317 3998 4.96 %
Rwork0.1974 76597 -
obs0.1991 80595 85.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 72.24 Å2
Refinement stepCycle: LAST / Resolution: 2.78→45.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16668 0 188 47 16903
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001917126
X-RAY DIFFRACTIONf_angle_d0.468423195
X-RAY DIFFRACTIONf_chiral_restr0.04022619
X-RAY DIFFRACTIONf_plane_restr0.0043094
X-RAY DIFFRACTIONf_dihedral_angle_d13.26546301
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.78-2.810.4191320.3493713X-RAY DIFFRACTION23.49
2.81-2.840.3572440.3414969X-RAY DIFFRACTION31.75
2.84-2.880.3689670.31941228X-RAY DIFFRACTION40.06
2.88-2.920.3303920.31791545X-RAY DIFFRACTION50.65
2.92-2.960.331030.32071888X-RAY DIFFRACTION62.01
2.96-30.33751080.31212244X-RAY DIFFRACTION73.34
3-3.040.34581170.32372494X-RAY DIFFRACTION81.09
3.04-3.090.44131500.33912622X-RAY DIFFRACTION85.48
3.09-3.140.4241180.32022714X-RAY DIFFRACTION87.76
3.14-3.20.34961420.28782693X-RAY DIFFRACTION89.26
3.2-3.260.35091540.27612805X-RAY DIFFRACTION91.36
3.26-3.320.29261210.27062888X-RAY DIFFRACTION92.73
3.32-3.390.33951310.25812893X-RAY DIFFRACTION93.97
3.39-3.460.2911570.26022909X-RAY DIFFRACTION95.04
3.46-3.540.27791530.24512962X-RAY DIFFRACTION96.35
3.54-3.630.26681750.24083024X-RAY DIFFRACTION98.49
3.63-3.730.3451590.27123010X-RAY DIFFRACTION98.69
3.73-3.840.23761760.19653055X-RAY DIFFRACTION99.97
3.84-3.960.23061530.17273071X-RAY DIFFRACTION100
3.96-4.10.18931560.16133081X-RAY DIFFRACTION99.97
4.1-4.270.19661770.14843048X-RAY DIFFRACTION99.94
4.27-4.460.18261640.14843061X-RAY DIFFRACTION99.94
4.46-4.690.16041810.14263085X-RAY DIFFRACTION100
4.69-4.990.16981690.1443068X-RAY DIFFRACTION99.97
4.99-5.370.2061460.16013078X-RAY DIFFRACTION99.94
5.37-5.910.22591680.17983105X-RAY DIFFRACTION99.88
5.91-6.760.21191710.18763075X-RAY DIFFRACTION99.88
6.77-8.510.20951570.16213127X-RAY DIFFRACTION99.97
8.52-45.510.16121570.16963142X-RAY DIFFRACTION99.19
Refinement TLS params.Method: refined / Origin x: -43.8422611776 Å / Origin y: 34.3575332171 Å / Origin z: -1.70056742832 Å
111213212223313233
T0.300952500671 Å20.00528698660956 Å20.00812992752477 Å2-0.257602290214 Å20.018391049095 Å2--0.377599711663 Å2
L0.266955742709 °20.00751540125033 °2-0.0115387020032 °2-0.193675790065 °2-0.0402011383613 °2--0.67096147535 °2
S-0.0153527024738 Å °0.00309612030758 Å °-0.0561951965663 Å °-0.0332720864192 Å °-0.00606512669311 Å °0.0303459891092 Å °0.045020056134 Å °-0.0197355912163 Å °0.0171569263906 Å °
Refinement TLS groupSelection details: all

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