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Yorodumi- PDB-1de0: MODULATING THE MIDPOINT POTENTIAL OF THE [4FE-4S] CLUSTER OF THE ... -
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-Basic information
Entry | Database: PDB / ID: 1de0 | ||||||
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Title | MODULATING THE MIDPOINT POTENTIAL OF THE [4FE-4S] CLUSTER OF THE NITROGENASE FE PROTEIN | ||||||
Components | NITROGENASE IRON PROTEIN | ||||||
Keywords | OXIDOREDUCTASE / REDOX PROTEINS / [FES] CLUSTERS / FE PROTEIN | ||||||
Function / homology | Function and homology information nitrogenase / carbonyl sulfide nitrogenase activity / nitrogenase activity / nitrogen fixation / 4 iron, 4 sulfur cluster binding / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Azotobacter vinelandii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.4 Å | ||||||
Authors | Jang, S.B. / Seefeldt, L.C. / Peters, J.W. | ||||||
Citation | Journal: Biochemistry / Year: 2000 Title: Modulating the midpoint potential of the [4Fe-4S] cluster of the nitrogenase Fe protein. Authors: Jang, S.B. / Seefeldt, L.C. / Peters, J.W. #1: Journal: Science / Year: 1992 Title: Crystallographic Structure of the Nitrogenase Iron Protein from Azotobacter vinelandii Authors: Georgiadis, M.M. / Komiya, H. / Chakrabarti, P. / Woo, D. / Kornuc, J.J. / Rees, D.C. #2: Journal: J.Mol.Biol. / Year: 1998 Title: Conformational Variability in Structures of the Nitrogenase Iron Proteins from Azotobacter vinelandii and Clostridium pasteurianum Authors: Schlessman, J.L. / Woo, D. / Joshua-Tor, L. / Howard, J.B. / Rees, D.C. #3: Journal: Nature / Year: 1997 Title: Structure of ADP x AlF4(-)-stabilized Nitrogenase Complex and its Implications for Signal Transduction Authors: Schindelin, H. / Kisker, C. / Schlessman, J.L. / 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 | 1de0.cif.gz | 124.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1de0.ent.gz | 96.6 KB | Display | PDB format |
PDBx/mmJSON format | 1de0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/de/1de0 ftp://data.pdbj.org/pub/pdb/validation_reports/de/1de0 | HTTPS FTP |
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-Related structure data
Related structure data | |
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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
#1: Protein | Mass: 31456.084 Da / Num. of mol.: 2 / Mutation: F135W / Source method: isolated from a natural source / Source: (natural) Azotobacter vinelandii (bacteria) / References: UniProt: P00459, nitrogenase #2: Chemical | ChemComp-SF4 / | #3: 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: 2.55 Å3/Da / Density % sol: 51.83 % | ||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: small tubes / pH: 8.5 Details: PEG 4000, 0.1 M TRIS HCL, 0.2 M SODIUM ACETATE, pH 8.5, SMALL TUBES, temperature 277K | ||||||||||||||||||||
Crystal grow | *PLUS 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: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Feb 15, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→20 Å / Num. all: 265157 / Num. obs: 24852 / % possible obs: 9.37 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 18.4 / Redundancy: 6 % / Biso Wilson estimate: 36.3 Å2 / Rmerge(I) obs: 0.077 |
Reflection shell | Resolution: 2.4→2.44 Å / Redundancy: 6 % / Rmerge(I) obs: 0.253 / % possible all: 0.2 |
Reflection | *PLUS % possible obs: 95.2 % / Num. measured all: 265157 |
Reflection shell | *PLUS % possible obs: 75.5 % / Mean I/σ(I) obs: 3.9 |
-Processing
Software |
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Refinement | Resolution: 2.4→20 Å / σ(F): 0 / σ(I): 0
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Refinement step | Cycle: LAST / Resolution: 2.4→20 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 50.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_deg / Dev ideal: 2.576 |