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Yorodumi- PDB-1pc5: Crystal Structure of the P50G Mutant of Ferredoxin I at 1.8 A Res... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1pc5 | ||||||
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Title | Crystal Structure of the P50G Mutant of Ferredoxin I at 1.8 A Resolution | ||||||
Components | Ferredoxin I | ||||||
Keywords | ELECTRON TRANSPORT / iron-sulfur protein / ferredoxin / mutant | ||||||
Function / homology | Function and homology information 3 iron, 4 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / electron transfer activity / DNA binding / metal ion binding Similarity search - Function | ||||||
Biological species | Azotobacter vinelandii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Camba, R. / Jung, Y.S. / Chen, K. / Hunsicker-Wang, L.M. / Burgess, B.K. / Stout, C.D. / Hirst, J. / Armstrong, F.A. | ||||||
Citation | Journal: Biochemistry / Year: 2003 Title: Mechanisms of redox-coupled proton transfer in proteins: role of the proximal proline in reactions of the [3Fe-4S] cluster in Azotobacter vinelandii ferredoxin I Authors: Camba, R. / Jung, Y.S. / Hunsicker-Wang, L.M. / Burgess, B.K. / Stout, C.D. / Hirst, J. / Armstrong, F.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1pc5.cif.gz | 44.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pc5.ent.gz | 30.3 KB | Display | PDB format |
PDBx/mmJSON format | 1pc5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pc/1pc5 ftp://data.pdbj.org/pub/pdb/validation_reports/pc/1pc5 | HTTPS FTP |
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-Related 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: 12150.662 Da / Num. of mol.: 1 / Mutation: P50G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Azotobacter vinelandii (bacteria) / Production host: Azotobacter vinelandii (bacteria) / References: UniProt: P00214 |
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#2: Chemical | ChemComp-SF4 / |
#3: Chemical | ChemComp-F3S / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 57.2 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 7.4 Details: Tris-HCl, Ammonium Sulfate, pH 7.4, VAPOR DIFFUSION, temperature 298K | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 2 ℃ / Method: vapor diffusionDetails: Shen, B., (1993) J.Biol.Chem., 268, 25928., Stout, C.D., (1979) J.Biol.Chem., 254, 3598. | |||||||||||||||||||||||||
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 / Wavelength: 1.5408 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 1, 2000 |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5408 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30 Å / Num. all: 14793 / Num. obs: 13643 / % possible obs: 92.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 1.8→1.85 Å / % possible all: 93.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→30 Å / Num. parameters: 5179 / Num. restraintsaints: 0 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 1%
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Refine analyze | Num. disordered residues: 3 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 932 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→30 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.8 Å / Rfactor Rfree: 0.253 / Rfactor Rwork: 0.179 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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