[English] 日本語
![](img/lk-miru.gif)
- PDB-6o7o: Nitrogenase MoFeP mutant F99Y/S188A from Azotobacter vinelandii i... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6o7o | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Nitrogenase MoFeP mutant F99Y/S188A from Azotobacter vinelandii in the dithionite reduced state after redox cycling | |||||||||
![]() | (Nitrogenase molybdenum-iron protein ...) x 2 | |||||||||
![]() | OXIDOREDUCTASE / Nitrogenase / F99Y / S188A / MoFeP | |||||||||
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 | ![]() ![]() ![]() | |||||||||
![]() | Rutledge, H.L. / Tezcan, F.A. | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 782.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 643 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 395.4 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 397.8 KB | Display | |
Data in XML | ![]() | 2.2 KB | Display | |
Data in CIF | ![]() | 31.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6o7lC ![]() 6o7mC ![]() 6o7nC ![]() 6o7pC ![]() 6o7qC ![]() 6o7rC ![]() 6o7sC ![]() 2minS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
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) ![]() #2: Protein | Mass: 59535.879 Da / Num. of mol.: 2 / Mutation: F99Y, S188A / Source method: isolated from a natural source / Source: (natural) ![]() |
---|
-Non-polymers , 5 types, 2015 molecules ![](data/chem/img/HCA.gif)
![](data/chem/img/ICS.gif)
![](data/chem/img/CLF.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ICS.gif)
![](data/chem/img/CLF.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.11 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 18% PEG 8000, 100 mM Tris pH 8.5, 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 |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 13, 2018 / Details: Flat Si Rh coated M0 |
Radiation | Monochromator: Liquid nitrogen-cooled double crystal Si(111) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5498 Å / Relative weight: 1 |
Reflection | Resolution: 1.89→79.8 Å / Num. obs: 147935 / % possible obs: 94 % / Redundancy: 6.3 % / Biso Wilson estimate: 15.88 Å2 / CC1/2: 0.987 / Rmerge(I) obs: 0.141 / Rpim(I) all: 0.092 / Rrim(I) all: 0.169 / Χ2: 0.95 / Net I/σ(I): 8 |
Reflection shell | Resolution: 1.89→1.92 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.867 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 7300 / CC1/2: 0.695 / Rpim(I) all: 0.582 / Rrim(I) all: 1.051 / Χ2: 0.68 / % possible all: 93.5 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 2MIN Resolution: 1.89→39.462 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.27 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.89→39.462 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|