+Open data
-Basic information
Entry | Database: PDB / ID: 1hqv | ||||||
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Title | STRUCTURE OF APOPTOSIS-LINKED PROTEIN ALG-2 | ||||||
Components | PROGRAMMED CELL DEATH PROTEIN 6 | ||||||
Keywords | APOPTOSIS / penta-EF-hand protein / calcium binding protein | ||||||
Function / homology | Function and homology information neural crest formation / vascular endothelial growth factor receptor-2 signaling pathway / neural crest cell development / COPII vesicle coat / COPII vesicle coating / negative regulation of TOR signaling / positive regulation of protein monoubiquitination / Cul3-RING ubiquitin ligase complex / negative regulation of vascular endothelial growth factor receptor signaling pathway / ubiquitin-like ligase-substrate adaptor activity ...neural crest formation / vascular endothelial growth factor receptor-2 signaling pathway / neural crest cell development / COPII vesicle coat / COPII vesicle coating / negative regulation of TOR signaling / positive regulation of protein monoubiquitination / Cul3-RING ubiquitin ligase complex / negative regulation of vascular endothelial growth factor receptor signaling pathway / ubiquitin-like ligase-substrate adaptor activity / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / endoplasmic reticulum to Golgi vesicle-mediated transport / endoplasmic reticulum exit site / protein-membrane adaptor activity / positive regulation of endothelial cell proliferation / positive regulation of endothelial cell migration / intracellular protein transport / response to calcium ion / calcium-dependent protein binding / positive regulation of angiogenesis / protein-macromolecule adaptor activity / cellular response to heat / cytoplasmic vesicle / angiogenesis / protein dimerization activity / endosome / apoptotic process / calcium ion binding / endoplasmic reticulum membrane / magnesium ion binding / endoplasmic reticulum / protein homodimerization activity / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.3 Å | ||||||
Authors | Jia, J. / Tarabykina, S. / Hansen, C. / Berchtold, M. / Cygler, M. | ||||||
Citation | Journal: Structure / Year: 2001 Title: Structure of apoptosis-linked protein ALG-2: insights into Ca2+-induced changes in penta-EF-hand proteins. Authors: Jia, J. / Tarabykina, S. / Hansen, C. / Berchtold, M. / Cygler, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1hqv.cif.gz | 51 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hqv.ent.gz | 36.4 KB | Display | PDB format |
PDBx/mmJSON format | 1hqv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hq/1hqv ftp://data.pdbj.org/pub/pdb/validation_reports/hq/1hqv | 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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2 |
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3 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 21888.396 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P12815 | ||
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#2: Chemical | ChemComp-CA / #3: 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: 2.71 Å3/Da / Density % sol: 54.66 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG 8000, Calcium Acetate, Sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||
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: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.04453 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 8, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.04453 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→30 Å / Num. all: 11288 / Num. obs: 10911 / % possible obs: 96.8 % / Redundancy: 6.4 % / Biso Wilson estimate: 50.16 Å2 / Rmerge(I) obs: 0.061 / Rsym value: 0.063 / Net I/σ(I): 23.7 |
Reflection shell | Resolution: 2.3→2.35 Å / Rmerge(I) obs: 0.213 / Num. unique all: 699 / Rsym value: 0.233 / % possible all: 96 |
Reflection | *PLUS Num. measured all: 69890 |
Reflection shell | *PLUS % possible obs: 96 % |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2.3→30 Å / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.3→30 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 44.7 Å2 | |||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_angle_deg / Dev ideal: 1.22 |