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Yorodumi- PDB-6wgs: Mycobacterium tuberculosis pduO-type ATP:cobalamin adenosyltransf... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6wgs | |||||||||
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Title | Mycobacterium tuberculosis pduO-type ATP:cobalamin adenosyltransferase bound to adenosylcobalamin | |||||||||
Components | Corrinoid adenosyltransferase | |||||||||
Keywords | TRANSFERASE / chaperone / B12 trafficking | |||||||||
Function / homology | Function and homology information corrinoid adenosyltransferase / corrinoid adenosyltransferase activity / porphyrin-containing compound biosynthetic process / cobalamin biosynthetic process / ATP binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Mycobacterium tuberculosis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | |||||||||
Authors | Mascarenhas, R.N. / Ruetz, M. / Koutmos, M. / Banerjee, R. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2020 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6wgs.cif.gz | 125.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6wgs.ent.gz | 96.4 KB | Display | PDB format |
PDBx/mmJSON format | 6wgs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wg/6wgs ftp://data.pdbj.org/pub/pdb/validation_reports/wg/6wgs | HTTPS FTP |
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-Related structure data
Related structure data | 6wguC 6wgvC 6wh5C 2g2dS S: Starting model for refinement 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 21000.648 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) Gene: E5M05_13560, ERS023446_03354, ERS027651_01619, FCN16_21305, SAMEA2682864_01680, SAMEA2683035_01578 Production host: Escherichia coli (E. coli) References: UniProt: A0A045JVI3, UniProt: P9WP99*PLUS, corrinoid adenosyltransferase |
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#2: Chemical | ChemComp-B12 / |
#3: Chemical | ChemComp-5AD / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.88 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 400 mM sodium phosphate monobasic/1600 mM potassium phosphate dibasic, 100 mM imidazole/HCl pH 8, and 200 mM sodium chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 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: 1.5→46.82 Å / Num. obs: 33103 / % possible obs: 100 % / Redundancy: 9.9 % / CC1/2: 0.999 / Net I/σ(I): 16.1 |
Reflection shell | Resolution: 1.5→1.53 Å / Rmerge(I) obs: 1.292 / Num. unique obs: 1609 / CC1/2: 0.764 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2G2D Resolution: 1.5→43.579 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 16.11 / 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: 88.85 Å2 / Biso mean: 29.7401 Å2 / Biso min: 12.57 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.5→43.579 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %
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Refinement TLS params. | Method: refined / Origin x: -30.2742 Å / Origin y: 25.0437 Å / Origin z: 16.088 Å
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Refinement TLS group |
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