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- PDB-8d32: Mycobacterium tuberculosis pduO-type ATP:cobalamin adenosyltransf... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8d32 | |||||||||
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Title | Mycobacterium tuberculosis pduO-type ATP:cobalamin adenosyltransferase bound to 5-deoxyadenosylrhodibalamin and PPPi | |||||||||
![]() | Corrinoid adenosyltransferase | |||||||||
![]() | TRANSFERASE / chaperone / B12 trafficking / rhodium | |||||||||
Function / homology | ![]() corrinoid adenosyltransferase / corrinoid adenosyltransferase activity / porphyrin-containing compound biosynthetic process / cobalamin biosynthetic process / ATP binding / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Mascarenhas, R.N. / Ruetz, M. / Koutmos, M. / Banerjee, R. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: A noble substitution leads to the cofactor mimicry by rhodibalamin Authors: Ruetz, M. / Mascarenhas, R.N. / Koutmos, M. / Krautler, B. / Banerjee, R. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 88.8 KB | Display | ![]() |
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PDB format | ![]() | 65.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 10.3 KB | Display | |
Data in CIF | ![]() | 13.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6wh5S S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 20718.373 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 37 molecules ![](data/chem/img/SF0.gif)
![](data/chem/img/5AD.gif)
![](data/chem/img/3PO.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/5AD.gif)
![](data/chem/img/3PO.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-SF0 / [ | ||
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#3: Chemical | ChemComp-5AD / | ||
#4: Chemical | ChemComp-3PO / | ||
#5: Chemical | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.41 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 30-32 % PEG 3350, 0.1 M bis Tris pH 6.5, 5 % glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 13, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1272 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→42.09 Å / Num. obs: 17763 / % possible obs: 99.9 % / Redundancy: 9.4 % / CC1/2: 0.995 / Rmerge(I) obs: 0.152 / Net I/σ(I): 7.5 |
Reflection shell | Resolution: 1.85→1.89 Å / Rmerge(I) obs: 0.932 / Num. unique obs: 1062 / CC1/2: 0.607 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6WH5 Resolution: 1.85→38.049 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.31 / 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: 75.74 Å2 / Biso mean: 39.9389 Å2 / Biso min: 18.55 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.85→38.049 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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