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Yorodumi- PDB-6o7o: Nitrogenase MoFeP mutant F99Y/S188A from Azotobacter vinelandii i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6o7o | |||||||||
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Title | Nitrogenase MoFeP mutant F99Y/S188A from Azotobacter vinelandii in the dithionite reduced state after redox cycling | |||||||||
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: 1.89 Å | |||||||||
Authors | Rutledge, H.L. / 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 | 6o7o.cif.gz | 782.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6o7o.ent.gz | 643 KB | Display | PDB format |
PDBx/mmJSON format | 6o7o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o7/6o7o ftp://data.pdbj.org/pub/pdb/validation_reports/o7/6o7o | HTTPS FTP |
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-Related structure data
Related structure data | 6o7lC 6o7mC 6o7nC 6o7pC 6o7qC 6o7rC 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 / 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 / Source: (natural) Azotobacter vinelandii (bacteria) / References: UniProt: P07329, nitrogenase |
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-Non-polymers , 5 types, 2015 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: 2.16 Å3/Da / Density % sol: 43.11 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 18% PEG 8000, 100 mM Tris pH 8.5, 500 mM NaCl, 10 mM dithionite. Protein was redox cycled with 5 mM indigo carmine and 10 mM dithionite prior to crystallization. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1.5498 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 13, 2018 / Details: Flat Si Rh coated M0 |
Radiation | Monochromator: Liquid nitrogen-cooled double crystal Si(111) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5498 Å / Relative weight: 1 |
Reflection | Resolution: 1.89→79.8 Å / Num. obs: 147935 / % possible obs: 94 % / Redundancy: 6.3 % / Biso Wilson estimate: 15.88 Å2 / CC1/2: 0.987 / Rmerge(I) obs: 0.141 / Rpim(I) all: 0.092 / Rrim(I) all: 0.169 / Χ2: 0.95 / Net I/σ(I): 8 |
Reflection shell | Resolution: 1.89→1.92 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.867 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 7300 / CC1/2: 0.695 / Rpim(I) all: 0.582 / Rrim(I) all: 1.051 / Χ2: 0.68 / % possible all: 93.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2MIN Resolution: 1.89→39.462 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.27 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.89→39.462 Å
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Refine LS restraints |
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LS refinement shell |
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