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Yorodumi- PDB-7ady: CO-removed state of the active site of vanadium nitrogenase VFe p... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ady | ||||||
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Title | CO-removed state of the active site of vanadium nitrogenase VFe protein | ||||||
Components | (Nitrogenase vanadium-iron protein ...) x 3 | ||||||
Keywords | OXIDOREDUCTASE / Nitrogenase / CO-turnover / CO-removal | ||||||
Function / homology | Function and homology information vanadium-iron nitrogenase complex / vanadium ion binding / nitrogenase / : / nitrogenase activity / nitrogen fixation / iron-sulfur cluster binding / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Azotobacter vinelandii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.05 Å | ||||||
Authors | Rohde, M. / Grunau, K. / Einsle, O. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2020 Title: CO Binding to the FeV Cofactor of CO-Reducing Vanadium Nitrogenase at Atomic Resolution. Authors: Rohde, M. / Grunau, K. / Einsle, O. #1: Journal: Angewandte Chemie / Year: 2020 Title: CO binding to the FeV Cofactor of CO-reducing Vanadium Nitrogenase at Atomic Resolution Authors: Rohde, M. / Grunau, K. / Einsle, O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ady.cif.gz | 969.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ady.ent.gz | 790.6 KB | Display | PDB format |
PDBx/mmJSON format | 7ady.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ady_validation.pdf.gz | 2.4 MB | Display | wwPDB validaton report |
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Full document | 7ady_full_validation.pdf.gz | 2.4 MB | Display | |
Data in XML | 7ady_validation.xml.gz | 104.3 KB | Display | |
Data in CIF | 7ady_validation.cif.gz | 159.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ad/7ady ftp://data.pdbj.org/pub/pdb/validation_reports/ad/7ady | HTTPS FTP |
-Related structure data
Related structure data | 7adrC 6feaS 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
-Nitrogenase vanadium-iron protein ... , 3 types, 6 molecules ADBECF
#1: Protein | Mass: 53951.559 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Azotobacter vinelandii (bacteria) / Gene: vnfD / Production host: Azotobacter vinelandii (bacteria) / References: UniProt: P16855, nitrogenase #2: Protein | Mass: 52839.465 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Azotobacter vinelandii (bacteria) / Gene: vnfK / Production host: Azotobacter vinelandii (bacteria) / References: UniProt: P16856, nitrogenase #3: Protein | Mass: 13387.959 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Azotobacter vinelandii (bacteria) / Gene: vnfG / Production host: Azotobacter vinelandii (bacteria) / References: UniProt: P16857, nitrogenase |
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-Non-polymers , 9 types, 2583 molecules
#4: Chemical | #5: Chemical | #6: Chemical | #7: Chemical | #8: Chemical | #9: Chemical | #10: Chemical | ChemComp-MG / #11: Chemical | ChemComp-EDO / #12: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 2.48 Å3/Da / Density % sol: 50.48 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: Tris/HCl pH 7.5, magnesium chloride, ethylene glycol, PEG 8000, sodium dithionite |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.9116 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jul 14, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9116 Å / Relative weight: 1 |
Reflection | Resolution: 1.05→46.66 Å / Num. obs: 1016322 / % possible obs: 94.1 % / Redundancy: 7 % / CC1/2: 0.999 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 1.05→1.07 Å / Num. unique obs: 40988 / CC1/2: 0.449 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6FEA Resolution: 1.05→46.66 Å / Cor.coef. Fo:Fc: 0.987 / Cor.coef. Fo:Fc free: 0.978 / SU B: 0.963 / SU ML: 0.019 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.02 / ESU R Free: 0.021 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 102.62 Å2 / Biso mean: 13.231 Å2 / Biso min: 4.49 Å2
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Refinement step | Cycle: final / Resolution: 1.05→46.66 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.05→1.077 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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