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- PDB-1fdd: AZOTOBACTER VINELANDII FERREDOXIN I: ASPARTATE 15 FACILITATES PRO... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1fdd | ||||||
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Title | AZOTOBACTER VINELANDII FERREDOXIN I: ASPARTATE 15 FACILITATES PROTON TRANSFER TO THE REDUCED [3FE-4S] CLUSTER | ||||||
![]() | FERREDOXIN | ||||||
![]() | ELECTRON TRANSPORT(IRON-SULFUR) | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() | ||||||
![]() | Stout, C.D. | ||||||
![]() | ![]() Title: Azotobacter vinelandii ferredoxin I. Aspartate 15 facilitates proton transfer to the reduced [3Fe-4S] cluster. Authors: Shen, B. / Martin, L.L. / Butt, J.N. / Armstrong, F.A. / Stout, C.D. / Jensen, G.M. / Stephens, P.J. / La Mar, G.N. / Gorst, C.M. / Burgess, B.K. #1: ![]() Title: Crystallographic Analysis of Two Site-Directed Mutants of Azotobacter Vinelandii Ferredoxin Authors: Soman, J. / Iismaa, S. / Stout, C.D. #2: ![]() 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: ![]() Title: Refinement of the 7 Fe Ferredoxin from Azotobacter at 1.9 Angstroms Resolution Authors: Stout, C.D. #5: ![]() 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: ![]() 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: ![]() 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: ![]() Title: Structure of a 7Fe Ferredoxin from Azotobacter Vinelandii Authors: Ghosh, D. / Fureyjunior, W. / O'Donnell, S. / Stout, C.D. #9: ![]() Title: Iron-Sulfur Clusters in Azotobacter Ferredoxin at 2.5 Angstroms Resolution Authors: Stout, C.D. / Ghosh, D. / Pattabhi, V. / Robbins, A.H. #10: ![]() Title: Structure of the Iron-Sulfur Clusters in Azotobacter Ferredoxin at 4.0 Angstroms Resolution Authors: Stout, C.D. #11: ![]() Title: Two Crystal Forms of Azotobacter Ferredoxin Authors: Stout, C.D. #12: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 34.8 KB | Display | ![]() |
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PDB format | ![]() | 23.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 395.5 KB | Display | ![]() |
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Full document | ![]() | 399.4 KB | Display | |
Data in XML | ![]() | 3.9 KB | Display | |
Data in CIF | ![]() | 5.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 12058.546 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() |
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#2: Chemical | ChemComp-SF4 / |
#3: Chemical | ChemComp-F3S / |
#4: Water | ChemComp-HOH / |
Sequence details | THE CHEMICAL SEQUENCE WAS DETERMINED IN COLLABORATION WITH J. B. HOWARD AND T. LORSBACH OF DEPT. OF ...THE CHEMICAL SEQUENCE WAS DETERMINED |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.07 Å3/Da / Density % sol: 59.95 % | |||||||||||||||||||||||||
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Crystal | *PLUS Density % sol: 55 % | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 2 ℃ / pH: 7.4 / Method: vapor diffusion / Details: referred to J.Biol.Chem. 254.3598-3599 1979 | |||||||||||||||||||||||||
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: 12536 / Num. obs: 11181 / % possible obs: 89 % / Num. measured all: 59292 / Rmerge(I) obs: 0.0595 |
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Processing
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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 Highest resolution: 1.9 Å / Lowest resolution: 8 Å / Num. reflection all: 10792 / σ(F): 0 / Rfactor all: 0.207 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_d / Dev ideal: 3.42 |