+Open data
-Basic information
Entry | Database: PDB / ID: 5crd | ||||||
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Title | Wild-type human skeletal calsequestrin | ||||||
Components | Calsequestrin-1 | ||||||
Keywords | Calcium Binding Protein | ||||||
Function / homology | Function and homology information terminal cisterna lumen / positive regulation of store-operated calcium channel activity / regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion / regulation of store-operated calcium entry / response to denervation involved in regulation of muscle adaptation / sarcoplasmic reticulum lumen / endoplasmic reticulum organization / sarcomere organization / protein polymerization / smooth endoplasmic reticulum ...terminal cisterna lumen / positive regulation of store-operated calcium channel activity / regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion / regulation of store-operated calcium entry / response to denervation involved in regulation of muscle adaptation / sarcoplasmic reticulum lumen / endoplasmic reticulum organization / sarcomere organization / protein polymerization / smooth endoplasmic reticulum / skeletal muscle tissue development / Ion homeostasis / T-tubule / sarcoplasmic reticulum membrane / : / positive regulation of release of sequestered calcium ion into cytosol / sarcoplasmic reticulum / Stimuli-sensing channels / Z disc / response to heat / mitochondrial matrix / calcium ion binding / endoplasmic reticulum / mitochondrion / identical protein binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 Å | ||||||
Authors | Lewis, K.M. / Ronish, L.A. / Kang, C. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2015 Title: Characterization of Two Human Skeletal Calsequestrin Mutants Implicated in Malignant Hyperthermia and Vacuolar Aggregate Myopathy. Authors: Lewis, K.M. / Ronish, L.A. / Rios, E. / Kang, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5crd.cif.gz | 92.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5crd.ent.gz | 67.7 KB | Display | PDB format |
PDBx/mmJSON format | 5crd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5crd_validation.pdf.gz | 430.5 KB | Display | wwPDB validaton report |
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Full document | 5crd_full_validation.pdf.gz | 431 KB | Display | |
Data in XML | 5crd_validation.xml.gz | 16.5 KB | Display | |
Data in CIF | 5crd_validation.cif.gz | 23.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cr/5crd ftp://data.pdbj.org/pub/pdb/validation_reports/cr/5crd | HTTPS FTP |
-Related structure data
Related structure data | 5creC 5crgC 5crhC 3trqS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 41722.578 Da / Num. of mol.: 1 / Fragment: residues 35-396 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CASQ1, CASQ / Production host: Escherichia coli (E. coli) / References: UniProt: P31415 | ||||
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#2: Chemical | ChemComp-CA / #3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.84 Å3/Da / Density % sol: 56.63 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 0.1 M MOPS, 27.5 % (v/v) 2-methyl-2,4-pentanediol, 0.2 M NaCl |
-Data collection
Diffraction | Mean temperature: 80 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: Jul 26, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.08→43.894 Å / Num. obs: 28782 / % possible obs: 99.37 % / Redundancy: 6.8 % / Net I/σ(I): 17.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3TRQ Resolution: 2.08→43.894 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.18 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 1.1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.08→43.894 Å
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Refine LS restraints |
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LS refinement shell |
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