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Yorodumi- PDB-5d8v: Ultra-high resolution structure of high-potential iron-sulfur protein -
+Open data
-Basic information
Entry | Database: PDB / ID: 5d8v | ||||||
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Title | Ultra-high resolution structure of high-potential iron-sulfur protein | ||||||
Components | High-potential iron-sulfur protein | ||||||
Keywords | METAL BINDING PROTEIN / iron-sulfur protein | ||||||
Function / homology | Function and homology information aerobic electron transport chain / 4 iron, 4 sulfur cluster binding / electron transfer activity / metal ion binding Similarity search - Function | ||||||
Biological species | Thermochromatium tepidum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.48 Å | ||||||
Authors | Hirano, Y. / Takeda, K. / Miki, K. | ||||||
Citation | Journal: Nature / Year: 2016 Title: Charge-density analysis of an iron-sulfur protein at an ultra-high resolution of 0.48 angstrom Authors: Hirano, Y. / Takeda, K. / Miki, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5d8v.cif.gz | 83.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5d8v.ent.gz | 64.4 KB | Display | PDB format |
PDBx/mmJSON format | 5d8v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d8/5d8v ftp://data.pdbj.org/pub/pdb/validation_reports/d8/5d8v | HTTPS FTP |
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-Related structure data
Related structure data | 3a39S 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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Unit cell |
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-Components
#1: Protein | Mass: 8793.851 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochromatium tepidum (bacteria) / References: UniProt: P80176 | ||||
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#2: Chemical | ChemComp-SF4 / | ||||
#3: Chemical | ChemComp-SO4 / #4: Chemical | #5: 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: 1.82 Å3/Da / Density % sol: 32.3 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4 Details: 1.6 M ammonium sulfate, 0.1 M sodium-citrate, 5 mM DTT |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.45086 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Feb 23, 2009 / Details: fiber-optic taper |
Radiation | Monochromator: Double-crystal Si(111) liquid-nitrogen-cooled Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.45086 Å / Relative weight: 1 |
Reflection | Resolution: 0.48→20 Å / Num. obs: 301119 / % possible obs: 96.3 % / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 61.1 |
Reflection shell | Resolution: 0.48→0.5 Å / Redundancy: 3 % / Rmerge(I) obs: 0.339 / Mean I/σ(I) obs: 2.7 / % possible all: 89 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3A39 Resolution: 0.48→20 Å / Cross valid method: FREE R-VALUE
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Displacement parameters | Biso mean: 6.19 Å2 | ||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.48→20 Å
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LS refinement shell | Resolution: 0.48→0.48 Å / Rfactor Rfree: 0.41 / Rfactor Rwork: 0.397 |