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Yorodumi- PDB-6nka: Crystal structure of Mycobacterium tuberculosis dethiobiotin synt... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6nka | ||||||
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Title | Crystal structure of Mycobacterium tuberculosis dethiobiotin synthetase in complex with 2'-deoxycytidine | ||||||
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: 2.23 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 2'-deoxycytidine Authors: Thompson, A.P. / Bruning, J.B. / Wegener, K.L. / 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 | 6nka.cif.gz | 183.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6nka.ent.gz | 143.9 KB | Display | PDB format |
PDBx/mmJSON format | 6nka.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6nka_validation.pdf.gz | 2.6 MB | Display | wwPDB validaton report |
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Full document | 6nka_full_validation.pdf.gz | 2.6 MB | Display | |
Data in XML | 6nka_validation.xml.gz | 38.6 KB | Display | |
Data in CIF | 6nka_validation.cif.gz | 55.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nk/6nka ftp://data.pdbj.org/pub/pdb/validation_reports/nk/6nka | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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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 (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P9WPQ5, dethiobiotin synthase #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-DCZ / #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: 2.41 Å3/Da / Density % sol: 48.93 % |
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Crystal grow | Temperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 1.2 - 1.7 M NaCitrate, 0.1M 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: MX2 / Wavelength: 0.9537 Å | ||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 21, 2016 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.23→49.01 Å / Num. obs: 44722 / % possible obs: 99.8 % / Redundancy: 14 % / Biso Wilson estimate: 25.41 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.032 / Rrim(I) all: 0.117 / Net I/σ(I): 13.5 / Num. measured all: 627582 / Scaling rejects: 4 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.23→49.014 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 30.93 / 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: 98.5 Å2 / Biso mean: 37.0368 Å2 / Biso min: 13.03 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.23→49.014 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: 16
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