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Yorodumi- PDB-7jt6: Mycobacterium tuberculosis dethiobiotin synthetase in complex wit... -
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-Basic information
Entry | Database: PDB / ID: 7jt6 | ||||||
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Title | Mycobacterium tuberculosis dethiobiotin synthetase in complex with Tetrazole 2 | ||||||
Components | ATP-dependent dethiobiotin synthetase BioD | ||||||
Keywords | LIGASE / inhibitor | ||||||
Function / homology | Function and homology information dethiobiotin synthase / dethiobiotin synthase activity / biotin biosynthetic process / magnesium ion binding / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å | ||||||
Authors | Pederick, J.P. / Bean, J.H. / Bruning, J.B. | ||||||
Citation | Journal: Acs Chem.Biol. / Year: 2021 Title: Inhibition of Mycobacterium tuberculosis Dethiobiotin Synthase ( Mt DTBS): Toward Next-Generation Antituberculosis Agents. Authors: Schumann, N.C. / Lee, K.J. / Thompson, A.P. / Salaemae, W. / Pederick, J.L. / Avery, T. / Gaiser, B.I. / Hodgkinson-Bean, J. / Booker, G.W. / Polyak, S.W. / Bruning, J.B. / Wegener, K.L. / Abell, A.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7jt6.cif.gz | 179 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7jt6.ent.gz | 140.1 KB | Display | PDB format |
PDBx/mmJSON format | 7jt6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7jt6_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 7jt6_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 7jt6_validation.xml.gz | 36.1 KB | Display | |
Data in CIF | 7jt6_validation.cif.gz | 50.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jt/7jt6 ftp://data.pdbj.org/pub/pdb/validation_reports/jt/7jt6 | HTTPS FTP |
-Related structure data
Related structure data | 7jt5C 7l1jC 6nmzS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 23285.664 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Strain: ATCC 25618 / H37Rv / Gene: bioD, Rv1570, MTCY336.33c / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P9WPQ5, dethiobiotin synthase #2: Chemical | ChemComp-VJG / {( #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.15 % |
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Crystal grow | Temperature: 289.15 K / Method: vapor diffusion, hanging drop Details: 1.2 - 1.7 M ammonium sulfate, 0.1 M Tris pH 8, 10-15% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Sep 21, 2019 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2→49.33 Å / Num. obs: 59724 / % possible obs: 100 % / Redundancy: 13.7 % / CC1/2: 1 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.028 / Rrim(I) all: 0.103 / Net I/σ(I): 18.2 / Num. measured all: 815941 / Scaling rejects: 3 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6NMZ Resolution: 2→48.05 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.83 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 77.76 Å2 / Biso mean: 43.171 Å2 / Biso min: 31.55 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2→48.05 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 21 / % reflection obs: 100 %
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