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Yorodumi- PDB-6nmz: Crystal structure of Mycobacterium tuberculosis dethiobiotin synt... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6nmz | ||||||
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Title | Crystal structure of Mycobacterium tuberculosis dethiobiotin synthetase in complex with an intentionally produced fragment degradation product B9D | ||||||
Components | ATP-dependent dethiobiotin synthetase BioD | ||||||
Keywords | TRANSFERASE / enzyme / synthetase / nucleotide triphosphate binding | ||||||
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: 2.4 Å | ||||||
Authors | Thompson, A.P. / Polyak, S.W. / Wegener, K.L. / Bruning, J.B. | ||||||
Funding support | Australia, 1items
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Citation | Journal: To Be Published Title: Crystal structure of Mycobacterium tuberculosis dethiobiotin synthetase in complex with an intentionally produced fragment degradation product B9D Authors: Thompson, A.P. / Polyak, S.W. / Wegener, K.L. / Bruning, J.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6nmz.cif.gz | 181 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6nmz.ent.gz | 143.6 KB | Display | PDB format |
PDBx/mmJSON format | 6nmz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nm/6nmz ftp://data.pdbj.org/pub/pdb/validation_reports/nm/6nmz | HTTPS FTP |
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-Related structure data
Related structure data | |
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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 / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P9WPQ5, dethiobiotin synthase #2: Chemical | ChemComp-KSJ / [( #3: Chemical | ChemComp-KSP / [( #4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | |
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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: 2.44 Å3/Da / Density % sol: 49.61 % |
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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: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 25, 2017 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.4→62.01 Å / Num. obs: 35543 / % possible obs: 97.4 % / Redundancy: 9.2 % / Biso Wilson estimate: 48.31 Å2 / CC1/2: 0.984 / Rmerge(I) obs: 0.261 / Rpim(I) all: 0.094 / Rrim(I) all: 0.279 / Net I/σ(I): 7 / Num. measured all: 325686 / Scaling rejects: 637 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→38.549 Å / SU ML: 0.48 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 33.23 / 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: 147.04 Å2 / Biso mean: 54.8494 Å2 / Biso min: 18.77 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.4→38.549 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13
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