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- PDB-7tpn: Selenium-incorporated nitrogenase Fe protein (Av2-Se) from A. vin... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7tpn | ||||||
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Title | Selenium-incorporated nitrogenase Fe protein (Av2-Se) from A. vinelandii (11 mM KSeCN) | ||||||
![]() | Nitrogenase iron protein 1 | ||||||
![]() | OXIDOREDUCTASE / nitrogenase / metalloprotein / iron sulfur cluster | ||||||
Function / homology | ![]() nitrogenase / : / nitrogenase activity / nitrogen fixation / 4 iron, 4 sulfur cluster binding / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Buscagan, T.M. / Kaiser, J.T. / Rees, D.C. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Selenocyanate derived Se-incorporation into the Nitrogenase Fe protein cluster. Authors: Buscagan, T.M. / Kaiser, J.T. / Rees, D.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 76.3 KB | Display | ![]() |
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PDB format | ![]() | 53 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7t4hC ![]() 7tneC ![]() 7tpoC ![]() 7tpvC ![]() 7tpwC ![]() 7tpxC ![]() 7tpyC ![]() 7tpzC ![]() 7tq0C ![]() 7tq9C ![]() 7tqcC ![]() 7tqeC ![]() 7tqfC ![]() 7tqhC ![]() 7tqiC ![]() 7tqjC ![]() 7tqkC ![]() 6n4lS 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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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 31548.240 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-Non-polymers , 5 types, 236 molecules ![](data/chem/img/SF4.gif)
![](data/chem/img/SFS.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ADP.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SFS.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ADP.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-SF4 / |
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#3: Chemical | ChemComp-SFS / |
#4: Chemical | ChemComp-MG / |
#5: Chemical | ChemComp-ADP / |
#6: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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Nonpolymer details | Individual instances of the Fe-S/Se cluster represented by residues 301 SF4 and 302 SFS may contain ...Individual instances of the Fe-S/Se cluster represented by residues 301 SF4 and 302 SFS may contain both sulfur and selenium. The primary citation should be consulted for a detailed description of the cluster refinement. |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.82 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 36-41% PEG400, 0.1-0.3 M sodium chloride, 0.1 M HEPES, pH 7.5, 2.5 mM dithionite, 0.17 mM Cymal-7 |
-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: Jun 29, 2021 | |||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 1.38→46.01 Å / Num. obs: 53696 / % possible obs: 99.6 % / Redundancy: 13 % / Biso Wilson estimate: 15.22 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.039 / Rrim(I) all: 0.101 / Net I/σ(I): 13.7 | |||||||||
Reflection shell | Resolution: 1.38→1.4 Å / Redundancy: 12.4 % / Rmerge(I) obs: 1.669 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 2653 / CC1/2: 0.775 / Rpim(I) all: 0.705 / Rrim(I) all: 1.816 / % possible all: 98.4 |
-Phasing
Phasing | Method: ![]() | ||||||
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Phasing MR | R rigid body: 0.429
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 6N4L Resolution: 1.38→46 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 21.51 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 75.31 Å2 / Biso mean: 21.9527 Å2 / Biso min: 9.86 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.38→46 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30
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