+Open data
-Basic information
Entry | Database: PDB / ID: 1n69 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of human saposin B | |||||||||
Components | SAPOSIN B | |||||||||
Keywords | LIPID BINDING PROTEIN / GLYCOSPHINGOLIPID ACTIVATOR PROTEIN | |||||||||
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 / sphingolipid metabolic process / prostate gland growth / 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 / sphingolipid metabolic process / prostate gland growth / 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 / lysosomal lumen / Peptide ligand-binding receptors / 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 / SYNCHROTRON / MAD / Resolution: 2.2 Å | |||||||||
Authors | Ahn, V.E. / Faull, K.F. / Whitelegge, J.P. / Fluharty, A.L. / Prive, G.G. | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2003 Title: Crystal Structure of saposin B reveals a dimeric shell for lipid binding Authors: Ahn, V.E. / Faull, K.F. / Whitelegge, J.P. / Fluharty, A.L. / Prive, G.G. #1: Journal: Protein Expr.Purif. / Year: 2003 Title: Expression, purification, crystallization and preliminary X-ray analysis of recombinant human saposin B Authors: Ahn, V.E. / Faull, K.F. / Whitelegge, J.P. / Higginson, J. / Fluharty, A.L. / Prive, G.G. | |||||||||
History |
| |||||||||
Remark 9 | BIOLOGICAL_UNIT: HOMODIMER | |||||||||
Remark 10 | OTHER DETAILS: METHIONINES SUBSTITUTED WITH SELENOMETHIONINE | |||||||||
Remark 600 | HETEROGEN The PEH ligand is disordered and is probably a mixture of phosphatidylethanolamines with ...HETEROGEN The PEH ligand is disordered and is probably a mixture of phosphatidylethanolamines with different acyl chain lengths. This ensemble has been modelled as a single phospholipid. As a result, the PEH atoms C2I, C3F, C3G, C3H and C3I are not present in this model. | |||||||||
Remark 5 | WARNING 1N69: THE PEH LIGAND IS DISORDERED | |||||||||
Remark 300 | BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 3 ... BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 3 CHAINS (A,B AND C). CHAINS A AND B FORM AN ASYMMETRIC HOMODIMER. CHAIN C FORMS A HOMODIMER WITH A CRYSTALLOGRAPHICALLY RELATED SYMMETRY MATE. SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1n69.cif.gz | 56.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1n69.ent.gz | 45.7 KB | Display | PDB format |
PDBx/mmJSON format | 1n69.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1n69_validation.pdf.gz | 701.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1n69_full_validation.pdf.gz | 708.9 KB | Display | |
Data in XML | 1n69_validation.xml.gz | 13.2 KB | Display | |
Data in CIF | 1n69_validation.cif.gz | 17.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n6/1n69 ftp://data.pdbj.org/pub/pdb/validation_reports/n6/1n69 | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 9128.529 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: Prosaposin, PSAP / Plasmid: PET-16(B) / Production host: Escherichia coli (E. coli) / Strain (production host): AD494(DE3) / References: UniProt: P07602 #2: Chemical | ChemComp-3PE / | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54 % | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.8 Details: POLYETHYLENE GLYCOL 3350, MAGNESIUM ACETATE, SODIUM CACODYLATE, PH 5.8, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K. THE CRYSTAL WAS TREATED WITH A MOTHER LIQUOR SOLUTION CONTAINING 0.1% ...Details: POLYETHYLENE GLYCOL 3350, MAGNESIUM ACETATE, SODIUM CACODYLATE, PH 5.8, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K. THE CRYSTAL WAS TREATED WITH A MOTHER LIQUOR SOLUTION CONTAINING 0.1% HYDROGEN PEROXIDE PRIOR TO FREEZING. | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Details: Ahn, V.E., (2003) Protein Expression Purif., 27, 186. | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 0.9789, 0.9793 | |||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 21, 2000 | |||||||||
Radiation | Protocol: MAD, SE-MET / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
| |||||||||
Reflection | Resolution: 2.2→37 Å / Num. all: 14644 / Num. obs: 14644 / % possible obs: 98.3 % / Redundancy: 10.5 % / Biso Wilson estimate: 22.7 Å2 / Rsym value: 0.059 / Net I/σ(I): 9 | |||||||||
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 5.3 % / Mean I/σ(I) obs: 2.6 / Num. unique all: 14644 / Rsym value: 0.289 / % possible all: 98.3 | |||||||||
Reflection | *PLUS Lowest resolution: 37 Å / Rmerge(I) obs: 0.059 | |||||||||
Reflection shell | *PLUS % possible obs: 98.3 % / Rmerge(I) obs: 0.289 |
-Processing
Software |
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MAD / Resolution: 2.2→19.74 Å / Rfactor Rfree error: 0.01 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 52.3682 Å2 / ksol: 0.321762 e/Å3 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.8 Å2
| ||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error free: 0.31 Å / Luzzati sigma a free: 0.22 Å | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→19.74 Å
| ||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||
LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
| ||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 20 Å / % reflection Rfree: 5 % | ||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||
Refine LS restraints | *PLUS
|