+Open data
-Basic information
Entry | Database: PDB / ID: 3bqq | ||||||
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Title | Crystal Structure of Human Saposin D (triclinic) | ||||||
Components | PROACTIVATOR POLYPEPTIDE | ||||||
Keywords | LIPID BINDING PROTEIN / SAPOSIN / SPHINGOLIPID ACTIVATOR PROTEIN / ACID CERAMIDASE / FARBER DISEASE / LIPID METABOLISM / LYSOSOME / SPHINGOLIPID METABOLISM | ||||||
Function / homology | Function and homology information positive regulation of beta-galactosidase activity / ganglioside GM1 transport to membrane / ganglioside GM2 binding / ganglioside GM3 binding / ganglioside GP1c binding / ganglioside GM1 binding / ganglioside GT1b binding / prostate gland growth / sphingolipid metabolic process / epithelial cell differentiation involved in prostate gland development ...positive regulation of beta-galactosidase activity / ganglioside GM1 transport to membrane / ganglioside GM2 binding / ganglioside GM3 binding / ganglioside GP1c binding / ganglioside GM1 binding / ganglioside GT1b binding / prostate gland growth / sphingolipid metabolic process / epithelial cell differentiation involved in prostate gland development / Glycosphingolipid catabolism / lysosomal transport / azurophil granule membrane / regulation of lipid metabolic process / enzyme activator activity / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / Peptide ligand-binding receptors / lysosomal lumen / regulation of autophagy / phospholipid binding / late endosome / Platelet degranulation / G alpha (i) signalling events / scaffold protein binding / collagen-containing extracellular matrix / protease binding / lysosome / lysosomal membrane / intracellular membrane-bounded organelle / Neutrophil degranulation / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Prive, G.G. / Popovic, K. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2008 Title: Structures of the human ceramide activator protein saposin D. Authors: Popovic, K. / Prive, G.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3bqq.cif.gz | 77.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bqq.ent.gz | 59.6 KB | Display | PDB format |
PDBx/mmJSON format | 3bqq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bq/3bqq ftp://data.pdbj.org/pub/pdb/validation_reports/bq/3bqq | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 8926.332 Da / Num. of mol.: 4 / Fragment: SAPOSIN D, RESIDUES 405-484 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PSAP / Plasmid: PET-16 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) ROSETTA-GAMI 2 / References: UniProt: P07602 #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: 2.84 Å3/Da / Density % sol: 56.75 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: PEG 4K, ZINC SULFATE, SODIUM ACETATE BUFFER, PH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 / Wavelength: 1.5418 Å |
Detector | Type: BRUKER SMART 6000 / Detector: CCD / Date: Mar 24, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→65 Å / Num. obs: 24429 / % possible obs: 92.6 % / Redundancy: 3.52 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 20.4 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.1406 / Mean I/σ(I) obs: 6.73 / % possible all: 91.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: SAPOSIN D P212121 Resolution: 2→64.55 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.92 / SU B: 3.71 / SU ML: 0.106 / Cross valid method: THROUGHOUT / ESU R: 0.185 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.496 Å2
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Refinement step | Cycle: LAST / Resolution: 2→64.55 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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