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Yorodumi- PDB-3min: NITROGENASE MOFE PROTEIN FROM AZOTOBACTER VINELANDII, OXIDIZED STATE -
+Open data
-Basic information
Entry | Database: PDB / ID: 3min | ||||||
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Title | NITROGENASE MOFE PROTEIN FROM AZOTOBACTER VINELANDII, OXIDIZED STATE | ||||||
Components | (NITROGENASE MOLYBDENUM IRON ...) x 2 | ||||||
Keywords | NITROGEN FIXATION / NITROGEN METABOLISM / OXIDOREDUCTASE / MOLYBDOENZYMES / BIOLOGICAL NITROGEN FIXATION | ||||||
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 / Resolution: 2.03 Å | ||||||
Authors | Peters, J.W. / Stowell, M.H.B. / Soltis, S.M. / Day, M.W. / Kim, J. / Rees, D.C. | ||||||
Citation | Journal: Biochemistry / Year: 1997 Title: Redox-dependent structural changes in the nitrogenase P-cluster. Authors: Peters, J.W. / Stowell, M.H. / Soltis, S.M. / Finnegan, M.G. / Johnson, M.K. / Rees, D.C. #1: Journal: Nature / Year: 1992 Title: Crystallographic Structure and Functional Implications of the Nitrogenase Molybdenum-Iron Protein from Azotobacter Vinelandii Authors: Kim, J. / Rees, D.C. #2: Journal: Science / Year: 1992 Title: Structural Models for the Metal Centers in the Nitrogenase Molybdenum-Iron Protein Authors: Kim, J. / 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 | 3min.cif.gz | 416.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3min.ent.gz | 332.1 KB | Display | PDB format |
PDBx/mmJSON format | 3min.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3min_validation.pdf.gz | 464.3 KB | Display | wwPDB validaton report |
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Full document | 3min_full_validation.pdf.gz | 511.2 KB | Display | |
Data in XML | 3min_validation.xml.gz | 42.7 KB | Display | |
Data in CIF | 3min_validation.cif.gz | 66.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mi/3min ftp://data.pdbj.org/pub/pdb/validation_reports/mi/3min | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
-NITROGENASE MOLYBDENUM IRON ... , 2 types, 4 molecules ACBD
#1: Protein | Mass: 55231.848 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Azotobacter vinelandii (bacteria) / Strain: WILD-TYPE / References: UniProt: P07328, nitrogenase #2: Protein | Mass: 59404.684 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Azotobacter vinelandii (bacteria) / Strain: WILD-TYPE / References: UniProt: P07329, nitrogenase |
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-Non-polymers , 5 types, 635 molecules
#3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | #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: 2.4 Å3/Da / Density % sol: 49 % | ||||||||||||||||||||||||
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Crystal grow | pH: 8.5 Details: PROTEIN WAS CRYSTALLIZED USING PRECIPITATING SOLUTION OF 30% PEG 4000, 0.2M NA2MO4, 0.1M TRIS PH 8.5 SOAKED IN SOAKED IN SODIUM DITHIONITE, 10MM FINAL CONC. | ||||||||||||||||||||||||
Crystal grow | *PLUS Method: batch method | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 1, 1996 / Details: PLATINUM MIRROR |
Radiation | Monochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 2.03→30 Å / Num. obs: 125145 / % possible obs: 92 % / Observed criterion σ(I): 1 / Redundancy: 4.6 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 16 |
Reflection shell | Resolution: 2.03→2.06 Å / Rmerge(I) obs: 0.162 / Mean I/σ(I) obs: 4 / % possible all: 77.1 |
Reflection | *PLUS Num. measured all: 576617 |
Reflection shell | *PLUS % possible obs: 77.1 % |
-Processing
Software |
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Refinement | Resolution: 2.03→30 Å / Cross valid method: THROUGHOUT / σ(F): 1
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Displacement parameters | Biso mean: 23.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.03→30 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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