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Yorodumi- PDB-3av8: Refined Structure of Plant-type [2Fe-2S] Ferredoxin I from Aphano... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3av8 | ||||||
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Title | Refined Structure of Plant-type [2Fe-2S] Ferredoxin I from Aphanothece sacrum at 1.46 A Resolution | ||||||
Components | Ferredoxin-1 | ||||||
Keywords | ELECTRON TRANSPORT / Beta-grasp / Redox Protein | ||||||
Function / homology | Function and homology information 2 iron, 2 sulfur cluster binding / electron transfer activity / metal ion binding Similarity search - Function | ||||||
Biological species | Aphanothece sacrum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 Å | ||||||
Authors | Kameda, H. / Hirabayashi, K. / Wada, K. / Fukuyama, K. | ||||||
Citation | Journal: Plos One / Year: 2011 Title: Mapping of protein-protein interaction sites in the plant-type [2Fe-2S] ferredoxin. Authors: Kameda, H. / Hirabayashi, K. / Wada, K. / Fukuyama, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3av8.cif.gz | 96 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3av8.ent.gz | 74.1 KB | Display | PDB format |
PDBx/mmJSON format | 3av8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/av/3av8 ftp://data.pdbj.org/pub/pdb/validation_reports/av/3av8 | HTTPS FTP |
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-Related structure data
Related structure data | 1fxiS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 10399.398 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aphanothece sacrum (bacteria) / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): C41DE3 / References: UniProt: P00250*PLUS #2: Chemical | ChemComp-FES / #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.79 % |
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Crystal grow | Temperature: 277 K / Method: microdialysis / pH: 7.5 Details: 70-80% ammonium sulfate, 0.1M TRIS, 0.7M sodium chloride, pH 7.5, MICRODIALYSIS, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Dec 15, 2010 |
Radiation | Monochromator: A Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.46→25 Å / Num. obs: 66810 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Biso Wilson estimate: 20.2 Å2 / Rsym value: 0.05 |
Reflection shell | Resolution: 1.46→1.51 Å / Redundancy: 5.5 % / Rsym value: 0.383 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1FXI Resolution: 1.46→24.64 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 269412.93 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 61.1651 Å2 / ksol: 0.405467 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.46→24.64 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.46→1.55 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
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Xplor file |
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