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Yorodumi- PDB-7tpv: Selenium-free nitrogenase Fe protein (Av2) from A. vinelandii (5m... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7tpv | ||||||
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Title | Selenium-free nitrogenase Fe protein (Av2) from A. vinelandii (5mM KSeCN Soaked) | ||||||
Components | Nitrogenase iron protein 1 | ||||||
Keywords | OXIDOREDUCTASE / nitrogenase / metalloprotein / iron sulfur cluster | ||||||
Function / homology | Function and homology information nitrogenase / carbonyl sulfide nitrogenase activity / nitrogenase activity / nitrogen fixation / 4 iron, 4 sulfur cluster binding / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Azotobacter vinelandii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.49 Å | ||||||
Authors | Buscagan, T.M. / Kaiser, J.T. / Rees, D.C. | ||||||
Funding support | United States, 1items
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Citation | Journal: Elife / Year: 2022 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7tpv.cif.gz | 74.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7tpv.ent.gz | 52.9 KB | Display | PDB format |
PDBx/mmJSON format | 7tpv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tp/7tpv ftp://data.pdbj.org/pub/pdb/validation_reports/tp/7tpv | HTTPS FTP |
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-Related structure data
Related structure data | 7t4hC 7tneC 7tpnC 7tpoC 7tpwC 7tpxC 7tpyC 7tpzC 7tq0C 7tq9C 7tqcC 7tqeC 7tqfC 7tqhC 7tqiC 7tqjC 7tqkC 6n4lS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-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
#1: Protein | Mass: 31548.240 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Azotobacter vinelandii (bacteria) / References: UniProt: P00459, nitrogenase |
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#2: Chemical | ChemComp-ADP / |
#3: Chemical | ChemComp-SF4 / |
#4: Chemical | ChemComp-MG / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.96 Å3/Da / Density % sol: 37.4 % |
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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, 5 mM potassium selenocyanate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97869, 0.98062 | |||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 12, 2021 | |||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 1.49→45.35 Å / Num. obs: 41143 / % possible obs: 99.4 % / Redundancy: 13 % / Biso Wilson estimate: 16.89 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.029 / Rrim(I) all: 0.076 / Net I/σ(I): 17.9 | |||||||||
Reflection shell | Resolution: 1.49→1.52 Å / Redundancy: 12.4 % / Rmerge(I) obs: 1.095 / Num. unique obs: 2448 / CC1/2: 0.877 / Rpim(I) all: 0.462 / Rrim(I) all: 1.191 / % possible all: 99.5 |
-Phasing
Phasing | Method: molecular replacement | ||||||
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Phasing MR | R rigid body: 0.507
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 6N4L Resolution: 1.49→38.7 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.45 / 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: 84.3 Å2 / Biso mean: 24.8388 Å2 / Biso min: 11.83 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.49→38.7 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 27
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