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Yorodumi- PDB-1m34: Nitrogenase Complex From Azotobacter Vinelandii Stabilized By ADP... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1m34 | ||||||
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Title | Nitrogenase Complex From Azotobacter Vinelandii Stabilized By ADP-Tetrafluoroaluminate | ||||||
Components |
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Keywords | OXIDOREDUCTASE / NITROGENASE / NITROGEN FIXATION / SIGNAL TRANSDUCTION / ELECTRON TRANSFER / ATP HYDROLYSIS / COMPLEX OF NITROGENASE PROTEINS | ||||||
Function / homology | Function and homology information molybdenum-iron nitrogenase complex / nitrogenase / : / nitrogenase activity / nitrogen fixation / iron-sulfur cluster binding / 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 / Resolution: 2.3 Å | ||||||
Authors | Schmid, B. / Einsle, O. / Chiu, H.-J. / Willing, A. / Yoshida, M. / Howard, J.B. / Rees, D.C. | ||||||
Citation | Journal: Biochemistry / Year: 2002 Title: Biochemical and Structural Characterization of the Crosslinked Complex of Nitrogenase: Comparison to the ADP-AlF4 Stabilized structure Authors: Schmid, B. / Einsle, O. / Chiu, H.-J. / Willing, A. / 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 | 1m34.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb1m34.ent.gz | 1008.1 KB | Display | PDB format |
PDBx/mmJSON format | 1m34.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1m34_validation.pdf.gz | 993.2 KB | Display | wwPDB validaton report |
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Full document | 1m34_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 1m34_validation.xml.gz | 134.8 KB | Display | |
Data in CIF | 1m34_validation.cif.gz | 206.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m3/1m34 ftp://data.pdbj.org/pub/pdb/validation_reports/m3/1m34 | HTTPS FTP |
-Related 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 | 2:1 Complex Of Homodimeric Fe-Protein and Heterotetrameric Mofe-Protein. There are two complexes in the asymmetric unit |
-Components
-Nitrogenase Molybdenum-Iron Protein ... , 2 types, 8 molecules ACIKBDJL
#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, UniProt: P07328*PLUS, 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, UniProt: P07329*PLUS, nitrogenase |
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-Protein , 1 types, 8 molecules EFGHMNOP
#3: Protein | Mass: 31417.045 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Azotobacter vinelandii (bacteria) References: UniProt: p00459, UniProt: P00459*PLUS, nitrogenase |
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-Non-polymers , 9 types, 1668 molecules
#4: Chemical | ChemComp-HCA / #5: Chemical | ChemComp-CFM / #6: Chemical | ChemComp-CA / #7: Chemical | ChemComp-CLF / #8: Chemical | ChemComp-MG / #9: Chemical | ChemComp-ALF / #10: Chemical | ChemComp-SF4 / #11: Chemical | ChemComp-ADP / #12: 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: 2.65 Å3/Da / Density % sol: 53.61 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 296 K / Method: liquid diffusion / pH: 6.5 Details: PEG 8000, cacodylate, magnesium chloride, pH 6.5, LIQUID DIFFUSION, temperature 296.0K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: batch method | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 1.005 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 11, 2001 / Details: double crystal monochromator |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.005 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→20 Å / Num. all: 273781 / Num. obs: 273781 / % possible obs: 83.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2.3→2.34 Å / % possible all: 66.9 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. measured all: 665961 / Rmerge(I) obs: 0.128 |
Reflection shell | *PLUS % possible obs: 66.9 % / Rmerge(I) obs: 0.266 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.3→20 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor Rwork: 0.2 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS |