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- PDB-7fdr: 7-FE FERREDOXIN FROM AZOTOBACTER VINELANDII, NA DITHIONITE REDUCE... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7fdr | ||||||||||||
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Title | 7-FE FERREDOXIN FROM AZOTOBACTER VINELANDII, NA DITHIONITE REDUCED, PH 8.5, 1.4A RESOLUTION, 100 K | ||||||||||||
![]() | PROTEIN (7-FE FERREDOXIN I) | ||||||||||||
![]() | 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 | ![]() | ||||||||||||
![]() | Schipke, C.G. / Goodin, D.B. / Mcree, D.E. / Stout, C.D. | ||||||||||||
![]() | ![]() Title: Oxidized and reduced Azotobacter vinelandii ferredoxin I at 1.4 A resolution: conformational change of surface residues without significant change in the [3Fe-4S]+/0 cluster. Authors: Schipke, C.G. / Goodin, D.B. / McRee, D.E. / 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 | ![]() | 90.2 KB | Display | ![]() |
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PDB format | ![]() | 66.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 440.8 KB | Display | ![]() |
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Full document | ![]() | 440.8 KB | Display | |
Data in XML | ![]() | 7.7 KB | Display | |
Data in CIF | ![]() | 10.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6fdrSC ![]() 7fd1C S: Starting model for refinement C: citing same article ( |
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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: 12059.530 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#2: Chemical | ChemComp-SF4 / |
#3: Chemical | ChemComp-F3S / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.88 Å3/Da / Density % sol: 57.27 % / Description: ALL DATA INCLUDING NEGATIVE I'S WERE USED | |||||||||||||||||||||||||
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Crystal grow | pH: 7.8 Details: PROTEIN CRYSTALLIZED FROM 60% SAT. AMMONIUM SULFATE, 0.4M TRIS-HCL, PH 7.8 | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7.4 / Method: unknown / Details: 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: ![]() |
Detector | Type: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Oct 1, 1997 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→100 Å / Num. obs: 17496 / % possible obs: 60.1 % / Redundancy: 2.28 % / Rsym value: 0.065 / Net I/σ(I): 15.4 |
Reflection shell | Resolution: 1.4→1.5 Å / Mean I/σ(I) obs: 1.1 / Rsym value: 0.31 / % possible all: 29.8 |
Reflection | *PLUS Num. measured all: 66520 / Rmerge(I) obs: 0.065 |
Reflection shell | *PLUS Highest resolution: 1.4 Å / Lowest resolution: 1.5 Å / % possible obs: 29.8 % / Rmerge(I) obs: 0.31 |
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Processing
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Refinement | Method to determine structure: OTHER Starting model: PDB ENTRY 6FDR Resolution: 1.4→100 Å / Num. parameters: 9013 / Num. restraintsaints: 10705 / σ(F): 0 / StereochEM target val spec case: FE CLUSTERS NOT RESTRAINED / Stereochemistry target values: ENGH & HUBER
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Solvent computation | Solvent model: MOEWS & KRETSINGER | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 2 / Occupancy sum hydrogen: 776 / Occupancy sum non hydrogen: 997.5 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→100 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.4 Å / Lowest resolution: 9999 Å / σ(F): 4 / Rfactor all: 0.17 / Rfactor obs: 0.148 / Rfactor Rwork: 0.17 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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