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- PDB-4m2p: Crystal structure of a non-myristoylated C39D recoverin mutant wi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4m2p | ||||||
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Title | Crystal structure of a non-myristoylated C39D recoverin mutant with one calcium ion bound to EF-hand 3 | ||||||
![]() | Recoverin![]() | ||||||
![]() | METAL BINDING PROTEIN / ![]() ![]() ![]() ![]() | ||||||
Function / homology | ![]() Inactivation, recovery and regulation of the phototransduction cascade / regulation of calcium ion transport / ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Prem Kumar, R. / Ranaghan, M.J. / Oprian, D.D. | ||||||
![]() | ![]() Title: A Highly Conserved Cysteine of Neuronal Calcium-sensing Proteins Controls Cooperative Binding of Ca2+ to Recoverin. Authors: Ranaghan, M.J. / Kumar, R.P. / Chakrabarti, K.S. / Buosi, V. / Kern, D. / Oprian, D.D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 58.3 KB | Display | ![]() |
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PDB format | ![]() | 41.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4m2oC ![]() 4m2qC ![]() 4mlwC ![]() 1omrS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | ![]() Mass: 23247.152 Da / Num. of mol.: 1 / Mutation: C39D Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-CA / |
#3: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.89 % |
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Crystal grow![]() | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 2.4 M SODIUM MALONATE, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 296K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 15, 2013 / Details: MIRRORS |
Radiation | Monochromator: DOUBLE CRYSTAL SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.45→32 Å / Num. obs: 36942 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Biso Wilson estimate: 66.4 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 1.45→1.53 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.421 / Mean I/σ(I) obs: 2.6 / % possible all: 100 |
-Phasing
Phasing![]() | Method: ![]() |
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Processing
Software |
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Refinement | Method to determine structure![]() ![]() Starting model: pdb entry 1OMR Resolution: 1.45→29.8 Å / Occupancy max: 1 / Occupancy min: 0.55 / SU ML: 0.16 / σ(F): 1.35 / Phase error: 22.28 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 62.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.45→29.8 Å
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Refine LS restraints |
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LS refinement shell |
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