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Yorodumi- PDB-5fd1: CRYSTAL STRUCTURES OF OXIDIZED AND REDUCED AZOTOBACTER VINELANDII... -
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-Basic information
Entry | Database: PDB / ID: 5fd1 | |||||||||
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Title | CRYSTAL STRUCTURES OF OXIDIZED AND REDUCED AZOTOBACTER VINELANDII FERREDOXIN AT PH 8 AND PH 6 | |||||||||
Components | FERREDOXIN | |||||||||
Keywords | ELECTRON TRANSPORT(IRON-SULFUR) | |||||||||
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: J.Biol.Chem. / Year: 1993 Title: Crystal structures of oxidized and reduced Azotobacter vinelandii ferredoxin at pH 8 and 6. Authors: Stout, C.D. #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: 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. #3: Journal: J.Mol.Biol. / Year: 1989 Title: Refinement of the 7 Fe Ferredoxin from Azotobacter at 1.9 Angstroms Resolution Authors: Stout, C.D. #5: 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. #6: 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. #7: 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. #8: 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. #9: 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. #10: 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. #11: Journal: J.Biol.Chem. / Year: 1979 Title: Two Crystal Forms of Azotobacter Ferredoxin Authors: Stout, C.D. #12: 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 | 5fd1.cif.gz | 34.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fd1.ent.gz | 23.4 KB | Display | PDB format |
PDBx/mmJSON format | 5fd1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fd/5fd1 ftp://data.pdbj.org/pub/pdb/validation_reports/fd/5fd1 | 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: 12059.530 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 / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3 Å3/Da / Density % sol: 59.06 % | |||||||||||||||||||||||||
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Crystal | *PLUS Density % sol: 55 % | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 2 ℃ / pH: 7.4 / Method: vapor diffusion / Details: Stout, C.D., (1979) J.Biol.Chem., 254, 3598. | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 20 Å / Num. all: 12058 / Num. obs: 9775 / % possible obs: 81.1 % / Num. measured all: 140232 / Rmerge(I) obs: 0.089 |
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Reflection shell | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 2.1 Å / % possible obs: 47.9 % |
-Processing
Software |
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Refinement | Resolution: 1.9→8 Å / σ(F): 0 /
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Refinement step | Cycle: LAST / Resolution: 1.9→8 Å
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Refine LS restraints |
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Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 17.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_plane_restr / Dev ideal: 1.58 |