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Yorodumi- PDB-6o7q: Nitrogenase MoFeP mutant S188A from Azotobacter vinelandii in the... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6o7q | |||||||||
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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 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 | 6o7q.cif.gz | 758.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6o7q.ent.gz | 625.6 KB | Display | PDB format |
PDBx/mmJSON format | 6o7q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o7/6o7q ftp://data.pdbj.org/pub/pdb/validation_reports/o7/6o7q | HTTPS FTP |
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-Related structure data
Related structure data | 6o7lC 6o7mC 6o7nC 6o7oC 6o7pC 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: 59519.879 Da / Num. of mol.: 2 / Mutation: 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, 1359 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: 2.21 Å3/Da / Density % sol: 44.43 % |
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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. 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: 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→48.684 Å / Num. obs: 135987 / % possible obs: 99.9 % / Redundancy: 6.4 % / Biso Wilson estimate: 20.243 Å2 / CC1/2: 0.985 / Rmerge(I) obs: 0.213 / Rpim(I) all: 0.137 / Rrim(I) all: 0.54 / Χ2: 0.94 / Net I/σ(I): 5.9 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 6.3 % / Rmerge(I) obs: 1.099 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 6741 / CC1/2: 0.709 / Rpim(I) all: 0.713 / Rrim(I) all: 1.315 / Χ2: 0.56 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2MIN Resolution: 2→48.684 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.84
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→48.684 Å
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Refine LS restraints |
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LS refinement shell |
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