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- PDB-6nn0: Crystal structure of Mycobacterium tuberculosis dethiobiotin synt... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6nn0 | ||||||
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Title | Crystal structure of Mycobacterium tuberculosis dethiobiotin synthetase in complex with 2'-deoxycytidine and fragment degradation product B9D | ||||||
![]() | ATP-dependent dethiobiotin synthetase BioD | ||||||
![]() | TRANSFERASE / enzyme / synthetase / nucleotide triphosphate binding | ||||||
Function / homology | ![]() dethiobiotin synthase / dethiobiotin synthase activity / biotin biosynthetic process / magnesium ion binding / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Thompson, A.P. / Polyak, S.W. / Wegener, K.L. / Bruning, J.B. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structure of Mycobacterium tuberculosis dethiobiotin synthetase in complex with 2'-deoxycytidine and B9D Authors: Thompson, A.P. / Polyak, S.W. / Wegener, K.L. / Bruning, J.B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 179.3 KB | Display | ![]() |
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PDB format | ![]() | 141.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.5 MB | Display | ![]() |
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Full document | ![]() | 2.5 MB | Display | |
Data in XML | ![]() | 37.9 KB | Display | |
Data in CIF | ![]() | 51.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 23285.664 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 25618 / H37Rv / Gene: bioD, Rv1570, MTCY336.33c / Plasmid: pET16b / Production host: ![]() ![]() |
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-Non-polymers , 5 types, 201 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/KSJ.gif)
![](data/chem/img/KSP.gif)
![](data/chem/img/CTN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/KSJ.gif)
![](data/chem/img/KSP.gif)
![](data/chem/img/CTN.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-KSJ / [( #4: Chemical | ChemComp-KSP / [( #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.85 % |
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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: ![]() | ||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 5, 2017 | ||||||||||||||||||||||||||||||
Radiation | Monochromator: Rigaku VariMax HF mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.34→87.68 Å / Num. obs: 37848 / % possible obs: 97.9 % / Redundancy: 11.6 % / Biso Wilson estimate: 49.81 Å2 / CC1/2: 0.984 / Rmerge(I) obs: 0.172 / Rpim(I) all: 0.052 / Rrim(I) all: 0.18 / Net I/σ(I): 9.2 / Num. measured all: 440918 / Scaling rejects: 3646 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 136.03 Å2 / Biso mean: 57.6978 Å2 / Biso min: 20.11 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.343→53.28 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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