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- PDB-6wgv: Mycobacterium tuberculosis pduO-type ATP:cobalamin adenosyltransf... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6wgv | |||||||||
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Title | Mycobacterium tuberculosis pduO-type ATP:cobalamin adenosyltransferase bound to adenosylcobalamin and PPPi | |||||||||
![]() | Corrinoid adenosyltransferase | |||||||||
![]() | TRANSFERASE / chaperone / B12 trafficking | |||||||||
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: Mobile loop dynamics in adenosyltransferase control binding and reactivity of coenzyme B 12 . Authors: Mascarenhas, R. / Ruetz, M. / McDevitt, L. / Koutmos, M. / 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 | ![]() | 84.2 KB | Display | ![]() |
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PDB format | ![]() | 61.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 9.7 KB | Display | |
Data in CIF | ![]() | 11.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6wgsC ![]() 6wguC ![]() 6wh5C ![]() 2g2dS S: Starting model for refinement C: citing same article ( |
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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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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 21000.648 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: E5M05_13560, ERS023446_03354, ERS027651_01619, FCN16_21305, SAMEA2682864_01680, SAMEA2683035_01578 Production host: ![]() ![]() References: UniProt: A0A045JVI3, UniProt: P9WP99*PLUS, corrinoid adenosyltransferase |
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-Non-polymers , 5 types, 19 molecules ![](data/chem/img/B12.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-B12 / |
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#3: Chemical | ChemComp-5AD / |
#4: Chemical | ChemComp-3PO / |
#5: Chemical | ChemComp-MG / |
#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: 2.45 Å3/Da / Density % sol: 49.83 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 26% PEG 3350, 0.1M bisTris 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 EIGER2 X 9M / Detector: PIXEL / Date: Aug 20, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→39.683 Å / Num. obs: 11342 / % possible obs: 99.1 % / Redundancy: 6.3 % / CC1/2: 0.972 / Rmerge(I) obs: 0.176 / Net I/σ(I): 6.6 |
Reflection shell | Resolution: 2.15→2.22 Å / Mean I/σ(I) obs: 2.2 / Num. unique obs: 906 / CC1/2: 0.712 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2G2D Resolution: 2.151→39.683 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.8 / 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: 151.42 Å2 / Biso mean: 44.5426 Å2 / Biso min: 16.99 Å2 | ||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.151→39.683 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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