+Open data
-Basic information
Entry | Database: PDB / ID: 6ug0 | |||||||||
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Title | N2-bound Nitrogenase MoFe-protein from Azotobacter vinelandii | |||||||||
Components | (Nitrogenase molybdenum-iron protein ...) x 2 | |||||||||
Keywords | OXIDOREDUCTASE / Azotobacter vinelandii / MoFe-protein / Fe-protein / FeMo-cofactor / oxidized P-cluster | |||||||||
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: 1.83 Å | |||||||||
Authors | Kang, W. / Hu, Y. / Ribbe, M.W. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Science / Year: 2020 Title: Structural evidence for a dynamic metallocofactor during N2reduction by Mo-nitrogenase. Authors: Kang, W. / Lee, C.C. / Jasniewski, A.J. / Ribbe, M.W. / Hu, Y. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ug0.cif.gz | 985.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ug0.ent.gz | 678.6 KB | Display | PDB format |
PDBx/mmJSON format | 6ug0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ug/6ug0 ftp://data.pdbj.org/pub/pdb/validation_reports/ug/6ug0 | HTTPS FTP |
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-Related structure data
Related structure data | 6vxtC 3u7qS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Azotobacter vinelandii (bacteria) / Gene: nifD / Production host: Azotobacter vinelandii (bacteria) / References: UniProt: P07328, nitrogenase #2: Protein | Mass: 59535.879 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Azotobacter vinelandii (bacteria) / Gene: nifK / Production host: Azotobacter vinelandii (bacteria) / References: UniProt: P07329, nitrogenase |
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-Non-polymers , 11 types, 809 molecules
#3: Chemical | #4: Chemical | ChemComp-ICE / | #5: Chemical | #6: Chemical | ChemComp-H2S / #7: Chemical | ChemComp-MO / #8: Chemical | #9: Chemical | #10: Chemical | ChemComp-GOL / #11: Chemical | ChemComp-PGE / | #12: Chemical | ChemComp-ICZ / | #13: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.92 Å3/Da / Density % sol: 57.85 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 14-19 % w/v PEG smear high, 0.16M ammonium acetate, 0.1M sodium citrate (pH 5.0), 25.6 % v/v glycerol, 5mM Eu(II)-EGTA |
-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: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 7, 2019 Details: Flat Si Rh coated M0, Kirkpatrick-Baez flat bent Si M1 & M2 |
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 Å / Relative weight: 1 |
Reflection | Resolution: 1.83→50 Å / Num. obs: 237283 / % possible obs: 95.2 % / Redundancy: 11.5 % / Biso Wilson estimate: 31.55 Å2 / CC1/2: 0.994 / Rpim(I) all: 0.061 / Rrim(I) all: 0.215 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 1.83→1.86 Å / Redundancy: 9 % / Num. unique obs: 225235 / CC1/2: 0.352 / Rpim(I) all: 1.035 / Rrim(I) all: 3.163 / % possible all: 94.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3U7Q Resolution: 1.83→39.19 Å / SU ML: 0.3038 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.6186 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 Details: Authors state that the electron density of metal clusters presented in validation report and wwPDB websites are calculated from general pipeline without applying specific geometry restraints ...Details: Authors state that the electron density of metal clusters presented in validation report and wwPDB websites are calculated from general pipeline without applying specific geometry restraints of the clusters. To reproduce accurate difference electron density map for the clusters, users should take the author-provided map coefficients presented in the structure factor file of the entry.
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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 mean: 49.87 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.83→39.19 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 30.9250854555 Å / Origin y: 118.258636614 Å / Origin z: 151.142986479 Å
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Refinement TLS group | Selection details: all |