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Yorodumi- PDB-6op2: Selenium incorporated FeMo-cofactor of nitrogenase from azotobact... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6op2 | |||||||||
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Title | Selenium incorporated FeMo-cofactor of nitrogenase from azotobacter vinelandii at high concentration of selenium | |||||||||
Components | (Nitrogenase molybdenum-iron protein ...) x 2 | |||||||||
Keywords | OXIDOREDUCTASE / nitrogenase / selenium / femo-cofactor | |||||||||
Function / homology | Function and homology information molybdenum-iron nitrogenase complex / 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: 1.9 Å | |||||||||
Authors | Arias, R.J. / Rees, D.C. | |||||||||
Funding support | United States, 2items
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Citation | Journal: J.Am.Chem.Soc. / Year: 2019 Title: Localized Electronic Structure of Nitrogenase FeMoco Revealed by Selenium K-Edge High Resolution X-ray Absorption Spectroscopy. Authors: Henthorn, J.T. / Arias, R.J. / Koroidov, S. / Kroll, T. / Sokaras, D. / Bergmann, U. / Rees, D.C. / DeBeer, S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6op2.cif.gz | 434.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6op2.ent.gz | 343.5 KB | Display | PDB format |
PDBx/mmJSON format | 6op2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6op2_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 6op2_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 6op2_validation.xml.gz | 80.6 KB | Display | |
Data in CIF | 6op2_validation.cif.gz | 117.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/op/6op2 ftp://data.pdbj.org/pub/pdb/validation_reports/op/6op2 | HTTPS FTP |
-Related structure data
Related structure data | 6op1C 6op3C 6op4C 3u7qS 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: 54000.559 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Azotobacter vinelandii (bacteria) / References: UniProt: P07328, nitrogenase #2: Protein | Mass: 59404.684 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Azotobacter vinelandii (bacteria) / References: UniProt: P07329, nitrogenase |
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-Non-polymers , 8 types, 1169 molecules
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-IMD / #6: Chemical | #7: Chemical | #8: Chemical | #9: Chemical | #10: 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: 2.32 Å3/Da / Density % sol: 47.06 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 26% v/v PEG6000, 0.75 M sodium chloride, 12.5% v/v MPD, 0.1 M imidazole/malate buffer, pH 8.0, 5 mM Na2S2O4 |
-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: 0.9791 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 7, 2017 |
Radiation | Monochromator: Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→37.81 Å / Num. obs: 160550 / % possible obs: 98.7 % / Redundancy: 3.5 % / CC1/2: 0.941 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.072 / Rrim(I) all: 0.137 / Net I/σ(I): 6.5 / Num. measured all: 561170 / Scaling rejects: 1084 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.288 / Num. measured all: 28155 / Num. unique obs: 7979 / CC1/2: 0.485 / Rpim(I) all: 0.183 / Rrim(I) all: 0.343 / Net I/σ(I) obs: 3.1 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3u7q Resolution: 1.9→37.81 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.917 / SU B: 3.499 / SU ML: 0.103 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.155 / ESU R Free: 0.14 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 101.81 Å2 / Biso mean: 15.21 Å2 / Biso min: 1.57 Å2
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Refinement step | Cycle: final / Resolution: 1.9→37.81 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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