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

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Basic information

Entry
Database: PDB / ID: 8oqr
TitleStructure of Mycobacterium tuberculosis beta-oxidation trifunctional enzyme in complex with Fragment-M-80
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 / enoyl-CoA hydratase activity / fatty acid beta-oxidation / acyltransferase activity, transferring groups other than amino-acyl groups / 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-cyanobenzenesulfonic acid / Putative acyltransferase Rv0859 / Probable fatty oxidation protein FadB
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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: Venkatesan, R. / 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_prop / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / software / struct_conf / struct_mon_prot_cis
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_prop.value / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_close_contact.dist / _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_free / _refine.ls_number_reflns_R_work / _refine.overall_SU_ML / _refine.pdbx_overall_phase_error / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _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_free / _refine_ls_shell.number_reflns_R_work / _refine_ls_shell.percent_reflns_obs / _struct_mon_prot_cis.pdbx_omega_angle
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)243,93330
Polymers240,9324
Non-polymers3,00126
Water7,999444
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14740 Å2
ΔGint-197 kcal/mol
Surface area85350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)250.702, 135.613, 120.892
Angle α, β, γ (deg.)90.000, 110.269, 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, 470 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-VWT / 4-cyanobenzenesulfonic acid


Mass: 183.184 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C7H5NO3S / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 444 / 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: 4 Å3/Da / Density % sol: 69.26 %
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: 2.4→117.589 Å / Num. obs: 118277 / % possible obs: 91.8 % / Redundancy: 6.5 % / Biso Wilson estimate: 48 Å2 / CC1/2: 0.982 / Net I/σ(I): 6.5
Reflection shellResolution: 2.4→2.637 Å / Num. unique obs: 9856 / CC1/2: 0.339

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
PHASERphasing
Cootmodel building
STARANISOdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→47.92 Å / SU ML: 0.3457 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 33.3455
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2596 5811 4.92 %
Rwork0.2197 112380 -
obs0.2217 118191 79.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.17 Å2
Refinement stepCycle: LAST / Resolution: 2.4→47.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16633 0 177 444 17254
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002417085
X-RAY DIFFRACTIONf_angle_d0.501423125
X-RAY DIFFRACTIONf_chiral_restr0.04122609
X-RAY DIFFRACTIONf_plane_restr0.00443074
X-RAY DIFFRACTIONf_dihedral_angle_d17.29746283
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.430.2958130.2954244X-RAY DIFFRACTION5.23
2.43-2.460.463340.2827473X-RAY DIFFRACTION10.35
2.46-2.490.306360.2841653X-RAY DIFFRACTION14.1
2.49-2.520.3376500.28541040X-RAY DIFFRACTION22.11
2.52-2.550.3276720.2961458X-RAY DIFFRACTION31.3
2.55-2.590.3049840.29741832X-RAY DIFFRACTION38.98
2.59-2.620.33521240.30472485X-RAY DIFFRACTION53.44
2.62-2.660.33191530.30173314X-RAY DIFFRACTION70.28
2.66-2.70.32381850.29263735X-RAY DIFFRACTION79.8
2.7-2.750.34632130.28984150X-RAY DIFFRACTION88.12
2.75-2.790.39812300.28784333X-RAY DIFFRACTION92.76
2.79-2.850.38412340.28414503X-RAY DIFFRACTION96.2
2.85-2.90.31482470.27594548X-RAY DIFFRACTION98.36
2.9-2.960.30282440.26234654X-RAY DIFFRACTION99.59
2.96-3.020.28182360.25754692X-RAY DIFFRACTION100
3.02-3.090.33582460.25734687X-RAY DIFFRACTION99.98
3.09-3.170.30222550.2624653X-RAY DIFFRACTION99.94
3.17-3.260.30682560.27024667X-RAY DIFFRACTION99.92
3.26-3.350.27942280.25624646X-RAY DIFFRACTION99.98
3.35-3.460.24552500.21984706X-RAY DIFFRACTION99.84
3.46-3.590.2662070.20164705X-RAY DIFFRACTION99.63
3.59-3.730.25042500.19884652X-RAY DIFFRACTION99.61
3.73-3.90.24382280.19414706X-RAY DIFFRACTION99.68
3.9-4.10.25032470.19054665X-RAY DIFFRACTION99.7
4.1-4.360.20692520.19264670X-RAY DIFFRACTION99.51
4.36-4.70.23192400.20224679X-RAY DIFFRACTION99.27
4.7-5.170.23412410.21444668X-RAY DIFFRACTION99.41
5.17-5.920.2622900.21784654X-RAY DIFFRACTION99.26
5.92-7.450.25312340.21564704X-RAY DIFFRACTION99.24
7.45-47.920.17992320.15734804X-RAY DIFFRACTION99.29
Refinement TLS params.Method: refined / Origin x: -44.3696626232 Å / Origin y: 34.3379963669 Å / Origin z: -1.61413019137 Å
111213212223313233
T0.242132265509 Å2-0.0129008279056 Å20.00633160968269 Å2-0.1689875999 Å20.0211216412492 Å2--0.279811121922 Å2
L0.046849665186 °20.00143797464837 °20.0214694639622 °2-0.109306455404 °20.105710174947 °2--0.601018339353 °2
S-0.0267972182411 Å °0.00487834269235 Å °-0.00784797976535 Å °-0.0308794215526 Å °0.000889310044997 Å °0.0236226178968 Å °-0.0295892638961 Å °0.0192096588451 Å °0.0248391273025 Å °
Refinement TLS groupSelection details: all

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