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- PDB-8e3u: Nickel-reconstituted nitrogenase MoFeP mutant S188A from Azotobac... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8e3u | |||||||||
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Title | Nickel-reconstituted nitrogenase MoFeP mutant S188A from Azotobacter vinelandii after IDS oxidation | |||||||||
![]() | (Nitrogenase molybdenum-iron protein ...) x 2 | |||||||||
![]() | OXIDOREDUCTASE / MoFeP / MoFe-protein | |||||||||
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 | ![]()
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![]() | ![]() Title: Role of Serine Coordination in the Structural and Functional Protection of the Nitrogenase P-Cluster. Authors: Rutledge, H.L. / Field, M.J. / Rittle, J. / Green, M.T. / Tezcan, F.A. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 748.9 KB | Display | ![]() |
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PDB format | ![]() | 615.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.9 MB | Display | ![]() |
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Full document | ![]() | 3 MB | Display | |
Data in XML | ![]() | 79.9 KB | Display | |
Data in CIF | ![]() | 115.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8e3tC ![]() 8e3vC ![]() 2minS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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: 55363.043 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Protein | Mass: 59519.879 Da / Num. of mol.: 2 / Mutation: S188A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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-Non-polymers , 6 types, 1019 molecules ![](data/chem/img/UFF.gif)
![](data/chem/img/HCA.gif)
![](data/chem/img/ICS.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HCA.gif)
![](data/chem/img/ICS.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | #7: Chemical | #8: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.17 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.25 Details: 18% PEG 8000, 100 mM Tris pH 8.25, 500 mM NaCl, 10 mM dithionite |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 2, 2018 | |||||||||
Radiation | Monochromator: Water-cooled flat double Si(111) Khozu monochromater Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 1.99→79.89 Å / Num. obs: 136546 / % possible obs: 99.8 % / Redundancy: 5.6 % / Biso Wilson estimate: 30.36 Å2 / CC1/2: 0.939 / Net I/σ(I): 3.4 | |||||||||
Reflection shell | Resolution: 1.99→2.02 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 0.5 / Num. unique obs: 6751 / CC1/2: 0.003 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2MIN Resolution: 1.99→79.89 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.27 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.99→79.89 Å
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Refine LS restraints |
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LS refinement shell |
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