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Yorodumi- PDB-1ff2: CRYSTAL STRUCTURE OF THE C42D MUTANT OF AZOTOBACTER VINELANDII 7F... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ff2 | ||||||
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Title | CRYSTAL STRUCTURE OF THE C42D MUTANT OF AZOTOBACTER VINELANDII 7FE FERREDOXIN (FDI) | ||||||
Components | FERREDOXIN I | ||||||
Keywords | ELECTRON TRANSPORT / 7Fe ferredoxin | ||||||
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: 2.3 Å | ||||||
Authors | Stout, C.D. / Burgess, B.K. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2000 Title: Structure of C42D Azotobacter vinelandii FdI. A Cys-X-X-Asp-X-X-Cys motif ligates an air-stable [4Fe-4S]2+/+ cluster Authors: Jung, Y.S. / Bonagura, C.A. / Tilley, G.J. / Gao-Sheridan, H.S. / Armstrong, F.A. / Stout, C.D. / Burgess, B.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ff2.cif.gz | 34.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ff2.ent.gz | 23.2 KB | Display | PDB format |
PDBx/mmJSON format | 1ff2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ff/1ff2 ftp://data.pdbj.org/pub/pdb/validation_reports/ff/1ff2 | HTTPS FTP |
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-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: 12071.476 Da / Num. of mol.: 1 / Mutation: C42D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Azotobacter vinelandii (bacteria) / Production host: Escherichia coli (E. coli) / 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: 2.87 Å3/Da / Density % sol: 57.09 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 7.8 Details: Ammonium sulfate, Tris-HCL, pH 7.8, VAPOR DIFFUSION, temperature 277.0K | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 2 ℃ / pH: 7.4 / Details: Shen, B., (1994) J.Biol.Chem., 269, 8564. | |||||||||||||||||||||||||
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: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: May 1, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→28 Å / Num. all: 48416 / Num. obs: 48416 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Biso Wilson estimate: 25 Å2 / Rmerge(I) obs: 0.171 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 2.3→2.34 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.78 / Num. unique all: 306 / % possible all: 99.7 |
Reflection | *PLUS Lowest resolution: 40 Å / Num. obs: 6640 / Num. measured all: 48416 |
Reflection shell | *PLUS % possible obs: 99.7 % / Mean I/σ(I) obs: 3.1 |
-Processing
Software |
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Refinement | Resolution: 2.3→23.8 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: X-Plor 3.8
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Refinement step | Cycle: LAST / Resolution: 2.3→23.8 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 23.8 Å / σ(F): 0 / % reflection Rfree: 5 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS |