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Yorodumi- PDB-6cvf: Crystal structure of Mycobacterium tuberculosis dethiobiotin synt... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6cvf | ||||||
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Title | Crystal structure of Mycobacterium tuberculosis dethiobiotin synthetase in complex with cytidine diphosphate | ||||||
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: 2.3 Å | ||||||
Authors | Thompson, A.P. / Bruning, J.B. / Wegener, K.L. / Polyak, S.W. | ||||||
Funding support | Australia, 1items
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Citation | Journal: Acs Catalysis / Year: 2018 Title: Mycobacterium tuberculosis Dethiobiotin Synthetase Facilitates Nucleoside Triphosphate Promiscuity through Alternate Binding Modes Authors: Thompson, A.P. / Salaemae, W. / Pederick, J.L. / Abell, A.D. / Booker, G.W. / Bruning, J.B. / Polyak, S.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6cvf.cif.gz | 198.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6cvf.ent.gz | 154.1 KB | Display | PDB format |
PDBx/mmJSON format | 6cvf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cv/6cvf ftp://data.pdbj.org/pub/pdb/validation_reports/cv/6cvf | HTTPS FTP |
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-Related structure data
Related structure data | 6cveC 6cvuC 6cvvC 6czbC 6czcC 6czeC 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: 23473.914 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-CDP / #3: Chemical | #4: 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: 49.69 % |
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Crystal grow | Temperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.7M NaCitrate, 0.1M Tris pH 7, 20% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.7108 Å | |||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Jul 7, 2017 | |||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 0.7108 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 2.3→51.69 Å / Num. obs: 39464 / % possible obs: 98.2 % / Redundancy: 6.9 % / Biso Wilson estimate: 22.53 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.113 / Net I/σ(I): 13.7 | |||||||||||||||||||||
Reflection shell |
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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: 2.3→49.577 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 0.32 / Phase error: 25.54
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 77.75 Å2 / Biso mean: 25.6835 Å2 / Biso min: 6.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.3→49.577 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: 15
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