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Yorodumi- PDB-4yi8: Crystal structure of non-myristoylated E153A recoverin at 1.2 A r... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4yi8 | ||||||
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Title | Crystal structure of non-myristoylated E153A recoverin at 1.2 A resolution with calcium ions bound to EF-hands 2 and 3 | ||||||
Components | Recoverin | ||||||
Keywords | Calcium binding protein / EF hand / NCS family | ||||||
Function / homology | Function and homology information Inactivation, recovery and regulation of the phototransduction cascade / regulation of calcium ion transport / phototransduction / photoreceptor outer segment / photoreceptor inner segment / visual perception / perikaryon / calcium ion binding / membrane / cytosol Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.2 Å | ||||||
Authors | Prem Kumar, R. / Ranaghan, M.J. / Oprian, D.D. | ||||||
Funding support | United States, 1items
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Citation | Journal: Biochemistry / Year: 2015 Title: Crystal Structure of Recoverin with Calcium Ions Bound to Both Functional EF Hands. Authors: Kumar, R.P. / Ranaghan, M.J. / Ganjei, A.Y. / Oprian, D.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4yi8.cif.gz | 134.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4yi8.ent.gz | 104.2 KB | Display | PDB format |
PDBx/mmJSON format | 4yi8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yi/4yi8 ftp://data.pdbj.org/pub/pdb/validation_reports/yi/4yi8 | HTTPS FTP |
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-Related structure data
Related structure data | 4yi9C 4mlwS 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: 23177.174 Da / Num. of mol.: 1 / Mutation: E153A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: RCVRN, RCV1 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): T7 EXPRESS (NEB) / References: UniProt: P21457 | ||||
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#2: Chemical | #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: 2.38 Å3/Da / Density % sol: 48.23 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 2.5 M Ammonium sulphate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 27, 2014 / Details: Mirrors |
Radiation | Monochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→48 Å / Num. obs: 64447 / % possible obs: 99.9 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 17.3 |
Reflection shell | Resolution: 1.2→1.26 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.346 / Mean I/σ(I) obs: 3.9 / % possible all: 99.1 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4MLW Resolution: 1.2→48 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 11.88 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 82.01 Å2 / Biso mean: 21.7524 Å2 / Biso min: 8.68 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.2→48 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 23
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