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Yorodumi- PDB-6o7r: Nitrogenase MoFeP mutant F99Y, S188A from Azotobacter vinelandii ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6o7r | |||||||||
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Title | Nitrogenase MoFeP mutant F99Y, S188A from Azotobacter vinelandii in the dithionite reduced state | |||||||||
Components | (Nitrogenase molybdenum-iron protein ...) x 2 | |||||||||
Keywords | OXIDOREDUCTASE / Nitrogenase / F99Y/S188A / MoFeP | |||||||||
Function / homology | Function and homology information molybdenum-iron nitrogenase complex / nitrogenase / carbonyl sulfide nitrogenase activity / 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: 2.27 Å | |||||||||
Authors | Rutledge, H.L. / Williamson, L.M. / Tezcan, F.A. | |||||||||
Funding support | United States, 2items
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Citation | Journal: J.Am.Chem.Soc. / Year: 2019 Title: Redox-Dependent Metastability of the Nitrogenase P-Cluster. Authors: Rutledge, H.L. / Rittle, J. / Williamson, L.M. / Xu, W.A. / Gagnon, D.M. / Tezcan, F.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6o7r.cif.gz | 758.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6o7r.ent.gz | 625.6 KB | Display | PDB format |
PDBx/mmJSON format | 6o7r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o7/6o7r ftp://data.pdbj.org/pub/pdb/validation_reports/o7/6o7r | HTTPS FTP |
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-Related structure data
Related structure data | 6o7lC 6o7mC 6o7nC 6o7oC 6o7pC 6o7qC 6o7sC 2minS 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 molybdenum-iron protein ... , 2 types, 4 molecules ACBD
#1: Protein | Mass: 55363.043 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: nifD / Source: (natural) Azotobacter vinelandii (bacteria) / References: UniProt: P07328, nitrogenase #2: Protein | Mass: 59535.879 Da / Num. of mol.: 2 / Mutation: F99Y, S188A / Source method: isolated from a natural source / Details: nifD / Source: (natural) Azotobacter vinelandii (bacteria) / References: UniProt: P07329, nitrogenase |
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-Non-polymers , 5 types, 1335 molecules
#3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
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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: 2.18 Å3/Da / Density % sol: 43.69 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 20% PEG 8000, 100 mM Tris pH 8.0, 500 mM NaCl, 10 mM dithionite |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.7388 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 29, 2018 / Details: Rh coated flat bent M0 |
Radiation | Monochromator: Si(111) and Si(220) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.7388 Å / Relative weight: 1 |
Reflection | Resolution: 2.27→79.84 Å / Num. obs: 82483 / % possible obs: 90.7 % / Redundancy: 5.8 % / CC1/2: 0.984 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.079 / Rrim(I) all: 0.14 / Χ2: 0.99 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 2.27→2.31 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.383 / Mean I/σ(I) obs: 3.8 / Num. unique obs: 4590 / CC1/2: 0.901 / Rpim(I) all: 0.269 / Rrim(I) all: 0.471 / Χ2: 0.96 / % possible all: 95.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2MIN Resolution: 2.27→47.311 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.51
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.27→47.311 Å
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Refine LS restraints |
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LS refinement shell |
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