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Yorodumi- PDB-5e1p: Ca(2+)-Calmodulin from Paramecium tetraurelia qFit disorder model -
+Open data
-Basic information
Entry | Database: PDB / ID: 5e1p | ||||||
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Title | Ca(2+)-Calmodulin from Paramecium tetraurelia qFit disorder model | ||||||
Components | Calmodulin | ||||||
Keywords | METAL BINDING PROTEIN / calcium signaling / calcium binding / EF hand | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Paramecium tetraurelia (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.01 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 | 5e1p.cif.gz | 194.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5e1p.ent.gz | 164.2 KB | Display | PDB format |
PDBx/mmJSON format | 5e1p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5e1p_validation.pdf.gz | 445.6 KB | Display | wwPDB validaton report |
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Full document | 5e1p_full_validation.pdf.gz | 446.2 KB | Display | |
Data in XML | 5e1p_validation.xml.gz | 11.6 KB | Display | |
Data in CIF | 5e1p_validation.cif.gz | 18.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e1/5e1p ftp://data.pdbj.org/pub/pdb/validation_reports/e1/5e1p | HTTPS FTP |
-Related structure data
Related structure data | 5e1kC 5e1nC 1exrS 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: 16687.420 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 (E. coli) / Strain (production host): JM109 / 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: 2.3 Å3/Da / Density % sol: 46.54 % |
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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: BL9-2 / Wavelength: 0.886 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 21, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.886 Å / Relative weight: 1 |
Reflection | Resolution: 1→25.52 Å / Num. obs: 78247 / % possible obs: 96.9 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 17.4 |
Reflection shell | Resolution: 1→1.04 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.506 / Mean I/σ(I) obs: 2.1 / % possible all: 83.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1EXR Resolution: 1.01→25.52 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 12.28 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.01→25.52 Å
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Refine LS restraints |
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LS refinement shell |
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