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Yorodumi- PDB-1fd2: SITE-DIRECTED MUTAGENESIS OF AZOTOBACTER VINELANDII FERREDOXIN I.... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1fd2 | ||||||
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Title | SITE-DIRECTED MUTAGENESIS OF AZOTOBACTER VINELANDII FERREDOXIN I. (FE-S) CLUSTER-DRIVEN PROTEIN REARRANGEMENT | ||||||
Components | FERREDOXIN | ||||||
Keywords | ELECTRON TRANSFER(IRON-SULFUR PROTEIN) | ||||||
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 / Resolution: 1.9 Å | ||||||
Authors | Stout, C.D. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 1990 Title: Site-directed mutagenesis of Azotobacter vinelandii ferredoxin I: [Fe-S] cluster-driven protein rearrangement. Authors: Martin, A.E. / Burgess, B.K. / Stout, C.D. / Cash, V.L. / Dean, D.R. / Jensen, G.M. / Stephens, P.J. #1: Journal: J.Biol.Chem. / Year: 1991 Title: Crystallographic Analysis of Two Site-Directed Mutants of Azotobacter Vinelandii Ferredoxin Authors: Soman, J. / Iismaa, S. / Stout, C.D. #2: Journal: J.Mol.Biol. / Year: 1989 Title: Refinement of the 7 Fe Ferredoxin from Azotobacter at 1.9 Angstroms Resolution Authors: Stout, C.D. #4: Journal: Proc.Natl.Acad.Sci.USA / Year: 1985 Title: (4Fe-4S)-Cluster-Depleted Azotobacter Vinelandii Ferredoxin I. A New 3Fe Iron-Sulfur Protein Authors: Stephens, P.J. / Morgan, T.V. / Devlin, F. / Penner-Hahn, J.E. / Hodgson, K.O. / Scott, R.A. / Stout, C.D. / Burgess, B.K. #5: Journal: J.Biol.Chem. / Year: 1983 Title: Structure of Azotobacter Vinelandii 7Fe Ferredoxin. Amino Acid Sequence and Electron Density Maps of Residues Authors: Howard, J.B. / Lorsbach, T.W. / Ghosh, D. / Melis, K. / Stout, C.D. #6: Journal: J.Mol.Biol. / Year: 1982 Title: Iron-Sulfur Clusters and Protein Structure of Azotobacter Ferredoxin at 2.0 Angstroms Resolution Authors: Ghosh, D. / O'Donnell, S. / Fureyjunior, W. / Robbins, A.H. / Stout, C.D. #7: Journal: J.Biol.Chem. / Year: 1981 Title: Structure of a 7Fe Ferredoxin from Azotobacter Vinelandii Authors: Ghosh, D. / Fureyjunior, W. / O'Donnell, S. / Stout, C.D. #8: Journal: J.Biol.Chem. / Year: 1980 Title: Iron-Sulfur Clusters in Azotobacter Ferredoxin at 2.5 Angstroms Resolution Authors: Stout, C.D. / Ghosh, D. / Pattabhi, V. / Robbins, A.H. #9: Journal: Am.Cryst.Assoc.,Abstr.Papers (Winter Meeting) / Year: 1979 Title: Structure of the Iron-Sulfur Clusters in Azotobacter Ferredoxin at 4.0 Angstroms Resolution Authors: Stout, C.D. #10: Journal: J.Biol.Chem. / Year: 1979 Title: Two Crystal Forms of Azotobacter Ferredoxin Authors: Stout, C.D. #11: Journal: Nature / Year: 1979 Title: Structure of the Iron-Sulphur Clusters in Azotobacter Ferredoxin at 4.0 Angstroms Resolution Authors: Stout, C.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1fd2.cif.gz | 35 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fd2.ent.gz | 23.7 KB | Display | PDB format |
PDBx/mmJSON format | 1fd2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1fd2_validation.pdf.gz | 402.9 KB | Display | wwPDB validaton report |
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Full document | 1fd2_full_validation.pdf.gz | 405.2 KB | Display | |
Data in XML | 1fd2_validation.xml.gz | 4 KB | Display | |
Data in CIF | 1fd2_validation.cif.gz | 5.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fd/1fd2 ftp://data.pdbj.org/pub/pdb/validation_reports/fd/1fd2 | HTTPS FTP |
-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: 12027.466 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Azotobacter vinelandii (bacteria) / References: UniProt: P00214 |
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#2: Chemical | ChemComp-SF4 / |
#3: Chemical | ChemComp-F3S / |
#4: Water | ChemComp-HOH / |
Compound details | THE STRUCTURE OF THIS MUTANT IS THE SAME AS THAT OF THE NATIVE EXEPT THAT RESIDUE 20 HAS CHANGED ...THE STRUCTURE OF THIS MUTANT IS THE SAME AS THAT OF THE NATIVE EXEPT THAT RESIDUE 20 HAS CHANGED FROM CYS TO ALA. THIS PROTEIN HAS A CUBANE-LIKE (3FE-4S) CLUSTER AND ALSO A STANDARD (4FE-4S) CLUSTER. THE (4FE-4S) CLUSTER HAS CYS 24 AS A LIGAND INSTEAD OF CYS 20 (NOW ALA 20) AND THE STRUCTURE IS REARRANGED |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3 Å3/Da / Density % sol: 58.96 % | |||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 2 ℃ / pH: 7.4 / Method: unknown | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 1.9 Å / Num. all: 11697 / Num. measured all: 55860 / Rmerge F obs: 0.095 |
-Processing
Software | Name: X-PLOR / Classification: refinement | ||||||||||||
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Refinement | Resolution: 1.9→8 Å /
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Refinement step | Cycle: LAST / Resolution: 1.9→8 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||
Refinement | *PLUS Rfactor Rwork: 0.232 | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS | ||||||||||||
Refine LS restraints | *PLUS Type: x_angle_d / Dev ideal: 3.67 |