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Yorodumi- PDB-6o7l: Nitrogenase MoFeP mutant S188A from Azotobacter vinelandii in the... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6o7l | |||||||||
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Title | Nitrogenase MoFeP mutant S188A from Azotobacter vinelandii in the dithionite reduced state after redox cycling | |||||||||
Components | (Nitrogenase molybdenum-iron protein ...) x 2 | |||||||||
Keywords | OXIDOREDUCTASE / Nitrogenase / 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: 2.26 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 | 6o7l.cif.gz | 729.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6o7l.ent.gz | 602.3 KB | Display | PDB format |
PDBx/mmJSON format | 6o7l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o7/6o7l ftp://data.pdbj.org/pub/pdb/validation_reports/o7/6o7l | HTTPS FTP |
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-Related structure data
Related structure data | 6o7mC 6o7nC 6o7oC 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) / Variant: DJ / References: UniProt: P07328, nitrogenase #2: Protein | Mass: 59519.879 Da / Num. of mol.: 2 / Mutation: S188A / Source method: isolated from a natural source / Source: (natural) Azotobacter vinelandii (bacteria) / Variant: DJ / References: UniProt: P07329, nitrogenase |
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-Non-polymers , 5 types, 272 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: 2.28 Å3/Da / Density % sol: 46.18 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 18% PEG 8000, 100 mM Tris pH 7.5, 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: ALS / Beamline: 5.0.2 / Wavelength: 1.7389 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 7, 2018 |
Radiation | Monochromator: Double-crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.7389 Å / Relative weight: 1 |
Reflection | Resolution: 2.26→49.422 Å / Num. obs: 97426 / % possible obs: 99.9 % / Redundancy: 6.5 % / Biso Wilson estimate: 32.234 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.178 / Rpim(I) all: 0.114 / Rrim(I) all: 0.212 / Χ2: 0.9 / Net I/σ(I): 5.9 |
Reflection shell | Resolution: 2.26→2.3 Å / Redundancy: 2.2 % / Rmerge(I) obs: 1.164 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 4788 / CC1/2: 0.845 / Rpim(I) all: 0.754 / Rrim(I) all: 1.392 / Χ2: 0.67 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2MIN Resolution: 2.26→49.422 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.61
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.26→49.422 Å
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Refine LS restraints |
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LS refinement shell |
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