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Yorodumi- PDB-6fdr: 7-FE FERREDOXIN FROM AZOTOBACTER VINELANDII AT 100K, NA DITHIONIT... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6fdr | |||||||||||||||
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Title | 7-FE FERREDOXIN FROM AZOTOBACTER VINELANDII AT 100K, NA DITHIONITE REDUCED AT PH 8.5, RESOLUTION 1.4 A | |||||||||||||||
Components | PROTEIN (7-FE FERREDOXIN I) | |||||||||||||||
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 / OTHER / Resolution: 1.4 Å | |||||||||||||||
Authors | Schipke, C.G. / Goodin, D.B. / Mcree, D.E. / Stout, C.D. | |||||||||||||||
Citation | Journal: Biochemistry / Year: 1999 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6fdr.cif.gz | 90 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6fdr.ent.gz | 66.1 KB | Display | PDB format |
PDBx/mmJSON format | 6fdr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fd/6fdr ftp://data.pdbj.org/pub/pdb/validation_reports/fd/6fdr | HTTPS FTP |
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-Related structure data
Related structure data | 7fd1C 7fdrC 6fd1S S: Starting model for refinement C: citing same article (ref.) |
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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: 12059.530 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) 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: 2.91 Å3/Da / Density % sol: 57.73 % / 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. CRYSTALS WERE SOAKED IN 5MM NA DITHIONITE, 0.15M TRIS/HCL PH 8.5 BEFORE DATA COLLECTION | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7.4 / Method: unknown | |||||||||||||||||||||||||
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: MACSCIENCE / Wavelength: 1.5418 |
Detector | Type: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Sep 1, 1998 |
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: 24027 / % possible obs: 82.8 % / Redundancy: 4.56 % / Rsym value: 0.15 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 1.4→1.5 Å / Mean I/σ(I) obs: 0.9 / Rsym value: 0.44 / % possible all: 55.3 |
Reflection | *PLUS Num. measured all: 109499 / Rmerge(I) obs: 0.104 |
Reflection shell | *PLUS % possible obs: 55.3 % / Rmerge(I) obs: 0.44 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER Starting model: PDB ENTRY 6FD1 Resolution: 1.4→100 Å / Num. parameters: 8990 / Num. restraintsaints: 10611 / 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: 1 / Occupancy sum hydrogen: 776 / Occupancy sum non hydrogen: 1000 | |||||||||||||||||||||||||||||||||
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 | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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