+Open data
-Basic information
Entry | Database: PDB / ID: 1m1n | ||||||
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Title | Nitrogenase MoFe protein from Azotobacter vinelandii | ||||||
Components | (Nitrogenase molybdenum-iron protein ...) x 2 | ||||||
Keywords | OXIDOREDUCTASE / atomic resolution / FeMo cofactor / nitrogen fixation / central nitrogen ligand | ||||||
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: 1.16 Å | ||||||
Authors | Einsle, O. / Tezcan, F.A. / Andrade, S.L.A. / Schmid, B. / Yoshida, M. / Howard, J.B. / Rees, D.C. | ||||||
Citation | Journal: Science / Year: 2002 Title: Nitrogenase MoFe-protein at 1.16 A resolution: a central ligand in the FeMo-cofactor. Authors: Einsle, O. / Tezcan, F.A. / Andrade, S.L. / Schmid, B. / Yoshida, M. / Howard, J.B. / 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 | 1m1n.cif.gz | 1.7 MB | Display | PDBx/mmCIF format |
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PDB format | pdb1m1n.ent.gz | 1.4 MB | Display | PDB format |
PDBx/mmJSON format | 1m1n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m1/1m1n ftp://data.pdbj.org/pub/pdb/validation_reports/m1/1m1n | HTTPS FTP |
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-Related structure data
Related structure data | 3minS 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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2 |
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Unit cell |
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Details | Biological assembly is a 2-(alpha),2-(beta) heterotetramer, i.e. half of the asymmetric unit. |
-Components
-Nitrogenase molybdenum-iron protein ... , 2 types, 8 molecules ACEGBDFH
#1: Protein | Mass: 55231.848 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Azotobacter vinelandii (bacteria) / References: UniProt: P07328, nitrogenase #2: Protein | Mass: 59404.684 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Azotobacter vinelandii (bacteria) / References: UniProt: P07329, nitrogenase |
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-Non-polymers , 5 types, 5037 molecules
#3: Chemical | ChemComp-HCA / #4: Chemical | ChemComp-CFN / #5: Chemical | ChemComp-CA / #6: Chemical | ChemComp-CLF / #7: Water | ChemComp-HOH / | |
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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: 2.35 Å3/Da / Density % sol: 47.6 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 Details: PEG 8000, sodium chloride, TRIS, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.992 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 18, 2002 |
Radiation | Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.992 Å / Relative weight: 1 |
Reflection | Resolution: 1.16→100 Å / Num. all: 1454519 / Num. obs: 1390520 / % possible obs: 95.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.5 % / Biso Wilson estimate: 12.34 Å2 / Rmerge(I) obs: 0.09 / Rsym value: 0.078 / Net I/σ(I): 10 |
Reflection shell | Resolution: 1.16→1.18 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.535 / Mean I/σ(I) obs: 1.6 / Num. unique all: 65290 / Rsym value: 0.554 / % possible all: 90 |
Reflection | *PLUS Lowest resolution: 50 Å / Num. measured all: 25851165 / Rmerge(I) obs: 0.09 |
Reflection shell | *PLUS % possible obs: 90 % / Rmerge(I) obs: 0.485 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3MIN Resolution: 1.16→50 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.982 / SU B: 1.41 / SU ML: 0.027 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.028 / ESU R Free: 0.029 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.839 Å2
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Refinement step | Cycle: LAST / Resolution: 1.16→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.16→1.19 Å / Total num. of bins used: 20 /
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Refinement | *PLUS Lowest resolution: 50 Å / Rfactor obs: 0.12349 / Rfactor Rfree: 0.149 / Rfactor Rwork: 0.123 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 1.16 Å / Lowest resolution: 1.19 Å / Rfactor Rfree: 0.309 / Rfactor Rwork: 0.275 |