+Open data
-Basic information
Entry | Database: PDB / ID: 7jrf | ||||||
---|---|---|---|---|---|---|---|
Title | CO-CO-BOUND NITROGENASE MOFE-PROTEIN FROM A. VINELANDII | ||||||
Components | (Nitrogenase molybdenum-iron protein ...) x 2 | ||||||
Keywords | OXIDOREDUCTASE / NITROGENASE / FEMO-COFACTOR / INHIBITION | ||||||
Function / homology | Function and homology information molybdenum-iron nitrogenase complex / nitrogenase / : / 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: 1.33 Å | ||||||
Authors | Spatzal, T. / Perez, K.A. / Buscagan, T.M. / Maggiolo, A.O. / Rees, D.C. | ||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2021 Title: Structural Characterization of Two CO Molecules Bound to the Nitrogenase Active Site. Authors: Buscagan, T.M. / Perez, K.A. / Maggiolo, A.O. / Rees, D.C. / Spatzal, T. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7jrf.cif.gz | 881.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7jrf.ent.gz | 717.9 KB | Display | PDB format |
PDBx/mmJSON format | 7jrf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7jrf_validation.pdf.gz | 2.4 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7jrf_full_validation.pdf.gz | 2.4 MB | Display | |
Data in XML | 7jrf_validation.xml.gz | 90 KB | Display | |
Data in CIF | 7jrf_validation.cif.gz | 139.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jr/7jrf ftp://data.pdbj.org/pub/pdb/validation_reports/jr/7jrf | HTTPS FTP |
-Related structure data
Related structure data | 3u7qS S: Starting model for refinement |
---|---|
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) Azotobacter vinelandii (bacteria) / References: UniProt: P07328, nitrogenase #2: Protein | Mass: 59535.879 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Azotobacter vinelandii (bacteria) / References: UniProt: P07329, nitrogenase |
---|
-Non-polymers , 9 types, 2050 molecules
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-IMD / #6: Chemical | #7: Chemical | ChemComp-CMO / #8: Chemical | #9: Chemical | #10: Chemical | #11: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.04 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Peg 4000, sodium chloride, imidazole / malate, glycerol, spermine |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9998 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 1, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9998 Å / Relative weight: 1 |
Reflection | Resolution: 1.33→39.63 Å / Num. obs: 447443 / % possible obs: 98.4 % / Redundancy: 5.1 % / Biso Wilson estimate: 14 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.041 / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 1.33→1.4 Å / Redundancy: 5 % / Rmerge(I) obs: 0.883 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 65111 / CC1/2: 0.747 / Rpim(I) all: 0.434 / % possible all: 98.1 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3U7Q Resolution: 1.33→39.63 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.977 / SU B: 1.948 / SU ML: 0.034 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.042 / ESU R Free: 0.042 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 87.98 Å2 / Biso mean: 14.493 Å2 / Biso min: 5.8 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.33→39.63 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.33→1.365 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|