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Yorodumi- PDB-1a8y: CRYSTAL STRUCTURE OF CALSEQUESTRIN FROM RABBIT SKELETAL MUSCLE SA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1a8y | ||||||
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Title | CRYSTAL STRUCTURE OF CALSEQUESTRIN FROM RABBIT SKELETAL MUSCLE SARCOPLASMIC RETICULUM AT 2.4 A RESOLUTION | ||||||
Components | CALSEQUESTRIN | ||||||
Keywords | CALCIUM-BINDING PROTEIN / CALSEQUESTRIN / SARCOPLASMIC RETICULUM / RABBIT SKELETAL MUSCLE | ||||||
Function / homology | Function and homology information 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 / sarcoplasmic reticulum lumen / ion binding / sarcomere organization / potassium ion binding / protein polymerization / sarcoplasmic reticulum membrane / positive regulation of release of sequestered calcium ion into cytosol ...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 / sarcoplasmic reticulum lumen / ion binding / sarcomere organization / potassium ion binding / protein polymerization / sarcoplasmic reticulum membrane / positive regulation of release of sequestered calcium ion into cytosol / sarcoplasmic reticulum / mitochondrial matrix / calcium ion binding / magnesium ion binding / protein homodimerization activity / metal ion binding Similarity search - Function | ||||||
Biological species | Oryctolagus cuniculus (rabbit) | ||||||
Method | X-RAY DIFFRACTION / MIR / Resolution: 2.4 Å | ||||||
Authors | Wang, S. / Trumble, W.R. / Liao, H. / Wesson, C.R. / Dunker, A.K. / Kang, C. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 1998 Title: Crystal structure of calsequestrin from rabbit skeletal muscle sarcoplasmic reticulum. Authors: Wang, S. / Trumble, W.R. / Liao, H. / Wesson, C.R. / Dunker, A.K. / Kang, C.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1a8y.cif.gz | 79.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1a8y.ent.gz | 60.1 KB | Display | PDB format |
PDBx/mmJSON format | 1a8y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a8/1a8y ftp://data.pdbj.org/pub/pdb/validation_reports/a8/1a8y | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 42468.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Organ: SKELETALSkeleton / Tissue: SKELETAL MUSCLE / References: UniProt: P07221 |
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#2: 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: 2.86 Å3/Da / Density % sol: 56.99 % | |||||||||||||||||||||||||
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Crystal grow | pH: 6.5 / Details: pH 6.5 | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Mar 1, 1997 / Details: MIRRORS |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→15 Å / Num. obs: 14812 / % possible obs: 80.1 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 23.34 Å2 / Rmerge(I) obs: 0.05 / Rsym value: 0.043 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 2.4→2.5 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.045 / Mean I/σ(I) obs: 4.6 / Rsym value: 0.303 / % possible all: 61.7 |
Reflection shell | *PLUS % possible obs: 61.7 % |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2.4→10 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 16.07 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→10 Å
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Refine LS restraints |
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.8 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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