[English] 日本語
Yorodumi- PDB-6op1: Selenium incorporated, carbon monoxide inhibited FeMo-cofactor of... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6op1 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Selenium incorporated, carbon monoxide inhibited FeMo-cofactor of azotobacter vinelandii | |||||||||
Components | (Nitrogenase molybdenum-iron protein ...) x 2 | |||||||||
Keywords | OXIDOREDUCTASE / nitrogenase / selenium / carbon monoxide | |||||||||
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: 1.7 Å | |||||||||
Authors | Arias, R.J. / Rees, D.C. | |||||||||
Funding support | United States, 2items
| |||||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6op1.cif.gz | 456.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6op1.ent.gz | 360 KB | Display | PDB format |
PDBx/mmJSON format | 6op1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/op/6op1 ftp://data.pdbj.org/pub/pdb/validation_reports/op/6op1 | HTTPS FTP |
---|
-Related structure data
Related structure data | 6op2C 6op3C 6op4C 3u7qS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-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 |
---|
-Non-polymers , 8 types, 1794 molecules
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-IMD / #6: Chemical | #7: Chemical | ChemComp-MG / #8: Chemical | #9: Chemical | #10: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.46 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9791 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 23, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→36.93 Å / Num. obs: 213040 / % possible obs: 98.6 % / Redundancy: 6.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.046 / Rrim(I) all: 0.124 / Net I/σ(I): 11 / Num. measured all: 1479527 / Scaling rejects: 1042 |
Reflection shell | Resolution: 1.7→1.73 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.571 / Num. measured all: 73217 / Num. unique obs: 10556 / CC1/2: 0.867 / Rpim(I) all: 0.233 / Rrim(I) all: 0.618 / Net I/σ(I) obs: 3.3 / % possible all: 98.8 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3u7q Resolution: 1.7→36.93 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.775 / SU ML: 0.058 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.085 / ESU R Free: 0.085 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 106.92 Å2 / Biso mean: 15.479 Å2 / Biso min: 3.39 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.7→36.93 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.7→1.744 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|