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- PDB-6op3: Selenium incorporated FeMo-cofactor of nitrogenase from Azotobact... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6op3 | |||||||||
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Title | Selenium incorporated FeMo-cofactor of nitrogenase from Azotobacter vinelandii with low concentration of selenium | |||||||||
![]() | (Nitrogenase molybdenum-iron protein ...) x 2 | |||||||||
![]() | OXIDOREDUCTASE / nitrogenase / femo-cofactor | |||||||||
Function / homology | ![]() molybdenum-iron nitrogenase complex / nitrogenase / : / nitrogenase activity / nitrogen fixation / iron-sulfur cluster binding / ATP binding / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Arias, R.J. / Rees, D.C. | |||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 466.1 KB | Display | ![]() |
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PDB format | ![]() | 367.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 91.3 KB | Display | |
Data in CIF | ![]() | 140.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6op1C ![]() 6op2C ![]() 6op4C ![]() 3u7qS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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) ![]() #2: Protein | Mass: 59404.684 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-Non-polymers , 8 types, 2176 molecules ![](data/chem/img/HCA.gif)
![](data/chem/img/ICS.gif)
![](data/chem/img/IMD.gif)
![](data/chem/img/SE.gif)
![](data/chem/img/CLF.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ICS.gif)
![](data/chem/img/IMD.gif)
![](data/chem/img/SE.gif)
![](data/chem/img/CLF.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-IMD / #6: Chemical | #7: Chemical | #8: Chemical | #9: Chemical | ChemComp-CA / #10: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.4 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop 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: ![]() ![]() ![]() |
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: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→37.85 Å / Num. obs: 269898 / % possible obs: 98.7 % / Redundancy: 3.4 % / CC1/2: 0.974 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.036 / Rrim(I) all: 0.068 / Net I/σ(I): 14.4 / Num. measured all: 909396 / Scaling rejects: 1235 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.202 / Num. measured all: 43441 / Num. unique obs: 13363 / CC1/2: 0.948 / Rpim(I) all: 0.134 / Rrim(I) all: 0.243 / Net I/σ(I) obs: 5.3 / % possible all: 98.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3u7q Resolution: 1.6→37.85 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.137 / SU ML: 0.04 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.066 / ESU R Free: 0.067 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: 66.36 Å2 / Biso mean: 13.612 Å2 / Biso min: 3.74 Å2
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Refinement step | Cycle: final / Resolution: 1.6→37.85 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.642 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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