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- PDB-8pf8: Structure of Mycobacterium tuberculosis beta-oxidation trifunctio... -

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Basic information

Entry
Database: PDB / ID: 8pf8
TitleStructure of Mycobacterium tuberculosis beta-oxidation trifunctional enzyme in complex with Fragment-M-72
Components
  • Probable fatty oxidation protein FadB
  • Putative acyltransferase Rv0859
KeywordsOXIDOREDUCTASE / fatty acid beta oxidation complex / mycobacterium tuberculosis / TFE / fragment screening / substrate channeling
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
Chem-JXL / Chem-YLN / Chem-YLZ / Chem-YMK / Putative acyltransferase Rv0859 / Probable fatty oxidation protein FadB
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.23 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.
History
DepositionJun 15, 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 / Author supporting evidence / 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_entity_instance_feature / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / struct_asym / struct_conf / struct_conn / struct_mon_prot_cis
Item: _entity.formula_weight / _entity.pdbx_description ..._entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _pdbx_entity_instance_feature.auth_comp_id / _pdbx_entity_instance_feature.comp_id / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _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 / _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_conf.end_auth_comp_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_comp_id / _struct_conf.end_label_seq_id / _struct_conf.pdbx_PDB_helix_length / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _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
Revision 2.2Oct 16, 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
A: Probable fatty oxidation protein FadB
B: Probable fatty oxidation protein FadB
C: Putative acyltransferase Rv0859
D: Putative acyltransferase Rv0859
hetero molecules


Theoretical massNumber of molelcules
Total (without water)246,01939
Polymers240,9324
Non-polymers5,08735
Water8,845491
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)250.961, 134.614, 119.974
Angle α, β, γ (deg.)90.000, 110.440, 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 Probable fatty oxidation protein FadB


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 , 7 types, 526 molecules

#3: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O3
#5: Chemical ChemComp-YMK / (2~{R})-3-bis[2-methyl-5-(trifluoromethyl)pyrazol-3-yl]boranyloxypropane-1,2-diol


Mass: 400.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H15BF6N4O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-YLZ / [(2~{R})-2,3-bis(oxidanyl)propoxy]-[2-methyl-5-(trifluoromethyl)pyrazol-3-yl]borinic acid


Mass: 267.998 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C8H12BF3N2O4 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-YLN / bis[2-methyl-5-(trifluoromethyl)pyrazol-3-yl]-bis(oxidanyl)boranuide


Mass: 343.013 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H10BF6N4O2 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical
ChemComp-JXL / [2-methyl-5-(trifluoromethyl)pyrazol-3-yl]boronic acid


Mass: 193.920 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C5H6BF3N2O2 / Feature type: SUBJECT OF INVESTIGATION
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 491 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 3.94 Å3/Da / Density % sol: 68.79 %
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: Diamond / Beamline: I04-1 / Wavelength: 0.91589 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91589 Å / Relative weight: 1
ReflectionResolution: 2.23→112.42 Å / Num. obs: 131177 / % possible obs: 95.7 % / Redundancy: 5.3 % / Biso Wilson estimate: 46.77 Å2 / CC1/2: 0.998 / Net I/σ(I): 11.5
Reflection shellResolution: 2.23→2.47 Å / Num. unique obs: 6560 / CC1/2: 0.623

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
autoPROCdata reduction
STARANISOdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.23→112.42 Å / SU ML: 0.314 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.7513
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2188 6593 5.03 %
Rwork0.1893 124574 -
obs0.1908 131167 72.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.56 Å2
Refinement stepCycle: LAST / Resolution: 2.23→112.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16728 0 394 491 17613
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002117399
X-RAY DIFFRACTIONf_angle_d0.513623607
X-RAY DIFFRACTIONf_chiral_restr0.04132641
X-RAY DIFFRACTIONf_plane_restr0.00433109
X-RAY DIFFRACTIONf_dihedral_angle_d12.59386387
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.23-2.260.338250.309448X-RAY DIFFRACTION0.9
2.26-2.290.445470.3236177X-RAY DIFFRACTION3.14
2.29-2.310.3479170.2853376X-RAY DIFFRACTION6.62
2.31-2.340.2609240.2749608X-RAY DIFFRACTION10.64
2.34-2.370.2884490.2832852X-RAY DIFFRACTION15.01
2.37-2.410.3078700.28961182X-RAY DIFFRACTION20.9
2.41-2.440.3055750.27441500X-RAY DIFFRACTION26.36
2.44-2.480.2986960.27621954X-RAY DIFFRACTION34.17
2.48-2.520.30841260.28512669X-RAY DIFFRACTION46.88
2.52-2.560.27881990.28093343X-RAY DIFFRACTION59.07
2.56-2.60.29912270.27324233X-RAY DIFFRACTION74.05
2.6-2.650.29242340.26815057X-RAY DIFFRACTION88.18
2.65-2.70.29063070.27515490X-RAY DIFFRACTION96.36
2.7-2.760.32013110.27955578X-RAY DIFFRACTION98.61
2.76-2.820.31363290.28185638X-RAY DIFFRACTION99.4
2.82-2.880.30383130.25965696X-RAY DIFFRACTION99.93
2.88-2.950.2873080.2485688X-RAY DIFFRACTION99.95
2.95-3.030.27042920.23455713X-RAY DIFFRACTION99.95
3.03-3.120.27713060.23745690X-RAY DIFFRACTION99.87
3.12-3.220.29232750.22745757X-RAY DIFFRACTION99.88
3.22-3.340.25072990.21995687X-RAY DIFFRACTION99.97
3.34-3.470.24433140.215725X-RAY DIFFRACTION99.95
3.47-3.630.24043010.18675720X-RAY DIFFRACTION99.9
3.63-3.820.20972770.17265713X-RAY DIFFRACTION99.77
3.82-4.060.19272950.14955718X-RAY DIFFRACTION99.9
4.06-4.370.16792770.13655743X-RAY DIFFRACTION99.72
4.37-4.810.1492950.13385712X-RAY DIFFRACTION99.22
4.81-5.510.17463140.14775735X-RAY DIFFRACTION99.8
5.51-6.940.18783450.16855716X-RAY DIFFRACTION99.95
6.94-112.420.15693060.15425856X-RAY DIFFRACTION99.55
Refinement TLS params.Method: refined / Origin x: -43.9419782662 Å / Origin y: 34.0679009283 Å / Origin z: -1.45770460614 Å
111213212223313233
T0.235984166749 Å2-0.00849074118895 Å2-0.00501622529393 Å2-0.227757674978 Å20.00665255583608 Å2--0.308082174233 Å2
L0.182877736863 °20.00200876770706 °2-0.0022389288923 °2-0.206124796498 °2-0.00372727893372 °2--0.558991108272 °2
S-0.00730930031742 Å °0.000842262701147 Å °-0.0260127305017 Å °-0.0294636841496 Å °-0.00539794478315 Å °0.0148633792081 Å °0.000704497518867 Å °-0.00975873034456 Å °0.0114068480235 Å °
Refinement TLS groupSelection details: all

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