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Yorodumi- PDB-1juo: Crystal Structure of Calcium-free Human Sorcin: A Member of the P... -
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-Basic information
Entry | Database: PDB / ID: 1juo | ||||||
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Title | Crystal Structure of Calcium-free Human Sorcin: A Member of the Penta-EF-Hand Protein Family | ||||||
Components | sorcin | ||||||
Keywords | METAL TRANSPORT / calcium-binding proteins / penta-ef-hand / PEF | ||||||
Function / homology | Function and homology information regulation of relaxation of muscle / regulation of high voltage-gated calcium channel activity / regulation of cell communication by electrical coupling / regulation of striated muscle contraction / negative regulation of cardiac muscle contraction / regulation of cardiac muscle cell contraction / Sodium/Calcium exchangers / Reduction of cytosolic Ca++ levels / muscle organ development / regulation of heart contraction ...regulation of relaxation of muscle / regulation of high voltage-gated calcium channel activity / regulation of cell communication by electrical coupling / regulation of striated muscle contraction / negative regulation of cardiac muscle contraction / regulation of cardiac muscle cell contraction / Sodium/Calcium exchangers / Reduction of cytosolic Ca++ levels / muscle organ development / regulation of heart contraction / negative regulation of heart rate / regulation of cell communication by electrical coupling involved in cardiac conduction / negative regulation of ryanodine-sensitive calcium-release channel activity / action potential / positive regulation of insulin secretion involved in cellular response to glucose stimulus / regulation of calcium ion transport / Ion transport by P-type ATPases / intracellular sequestering of iron ion / calcium channel regulator activity / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / Ion homeostasis / sarcoplasmic reticulum membrane / T-tubule / positive regulation of release of sequestered calcium ion into cytosol / sarcoplasmic reticulum / Stimuli-sensing channels / Z disc / calcium ion transport / heart development / DNA-binding transcription factor binding / protease binding / transmembrane transporter binding / protein heterodimerization activity / signaling receptor binding / calcium ion binding / endoplasmic reticulum membrane / signal transduction / extracellular exosome / nucleoplasm / identical protein binding / membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MIR / Resolution: 2.2 Å | ||||||
Authors | Xie, X. | ||||||
Citation | Journal: Protein Sci. / Year: 2001 Title: Crystal structure of calcium-free human sorcin: a member of the penta-EF-hand protein family. Authors: Xie, X. / Dwyer, M.D. / Swenson, L. / Parker, M.H. / Botfield, M.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1juo.cif.gz | 83.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1juo.ent.gz | 64 KB | Display | PDB format |
PDBx/mmJSON format | 1juo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1juo_validation.pdf.gz | 370.4 KB | Display | wwPDB validaton report |
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Full document | 1juo_full_validation.pdf.gz | 375.8 KB | Display | |
Data in XML | 1juo_validation.xml.gz | 8.4 KB | Display | |
Data in CIF | 1juo_validation.cif.gz | 13.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ju/1juo ftp://data.pdbj.org/pub/pdb/validation_reports/ju/1juo | HTTPS FTP |
-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: 21695.336 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P30626 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.44 Å3/Da / Density % sol: 64.26 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: sodium chloride, HEPES, EGTA, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 64 % | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 30, 1999 / Details: mirrors |
Radiation | Monochromator: Confocal Multilayer (Rigaku/MSC) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. all: 167295 / Num. obs: 28472 / % possible obs: 90.7 % / Observed criterion σ(I): -1 / Biso Wilson estimate: 32.1 Å2 / Rmerge(I) obs: 0.064 |
Reflection shell | Resolution: 2.2→2.26 Å / Rmerge(I) obs: 0.491 / Mean I/σ(I) obs: 2.1 / Num. unique all: 1929 / % possible all: 75.3 |
Reflection | *PLUS Num. measured all: 167295 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2.2→37.56 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 368354.7 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: RESOLUTION-DEPENDENT WEIGHTING SCHEME USED. BULK SOLVENT MODEL USED.
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Solvent computation | Solvent model: flat model / Bsol: 41.8194 Å2 / ksol: 0.294676 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→37.56 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNX2000 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 9.9 % / Rfactor obs: 0.212 / Rfactor Rfree: 0.256 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 47.1 Å2 | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.363 / % reflection Rfree: 10.3 % / Rfactor Rwork: 0.347 |