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Yorodumi- PDB-5e1k: Selenomethionine Ca2+-Calmodulin from Paramecium tetraurelia SAD data -
+Open data
-Basic information
Entry | Database: PDB / ID: 5e1k | ||||||
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Title | Selenomethionine Ca2+-Calmodulin from Paramecium tetraurelia SAD data | ||||||
Components | Calmodulin | ||||||
Keywords | METAL BINDING PROTEIN / calcium signaling / EF hand / calcium binding | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Paramecium tetraurelia (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1 Å | ||||||
Authors | Lin, J. / van den Bedem, H. / Brunger, A.T. / Wilson, M.A. | ||||||
Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2016 Title: Atomic resolution experimental phase information reveals extensive disorder and bound 2-methyl-2,4-pentanediol in Ca(2+)-calmodulin. Authors: Lin, J. / van den Bedem, H. / Brunger, A.T. / Wilson, M.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5e1k.cif.gz | 104.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5e1k.ent.gz | 80.9 KB | Display | PDB format |
PDBx/mmJSON format | 5e1k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e1/5e1k ftp://data.pdbj.org/pub/pdb/validation_reports/e1/5e1k | HTTPS FTP |
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-Related structure data
Related structure data | 5e1nC 5e1pC 1exrS C: citing same article (ref.) 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: 17062.580 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Paramecium tetraurelia (eukaryote) / Gene: CAM, GSPATT00015825001 / Plasmid: pkk233-3 / Production host: Escherichia coli / Strain (production host): B834 / References: UniProt: P07463 | ||||
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#2: Chemical | ChemComp-CA / #3: Chemical | #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: 2.25 Å3/Da / Density % sol: 45.33 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 50 mM sodium cacodylate, 50% MPD |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.9785 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 4, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 |
Reflection | Resolution: 1→25 Å / Num. obs: 75551 / % possible obs: 94 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.121 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 1→1.02 Å / Redundancy: 3.8 % / Rmerge(I) obs: 2.19 / Mean I/σ(I) obs: 1.6 / % possible all: 84.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1EXR Resolution: 1→25 Å / Num. parameters: 16557 / Num. restraintsaints: 28137 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
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Solvent computation | Solvent model: BABINET | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 79 / Occupancy sum hydrogen: 1066 / Occupancy sum non hydrogen: 1321.8 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1→25 Å
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Refine LS restraints |
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