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- PDB-1n69: Crystal structure of human saposin B -

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Basic information

Entry
Database: PDB / ID: 1n69
TitleCrystal structure of human saposin B
ComponentsSAPOSIN B
KeywordsLIPID 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 / prostate gland growth / sphingolipid metabolic process / Glycosphingolipid catabolism ...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 / Glycosphingolipid catabolism / epithelial cell differentiation involved in prostate gland development / 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
Saposin, chordata / Saposin-like / NK-Lysin / Saposin A-type domain / Saposin / Saposin A-type domain / Saposin A-type domain profile. / Saposin/surfactant protein-B A-type DOMAIN / Saposin-like type B, region 1 / Saposin-like type B, region 1 ...Saposin, chordata / Saposin-like / NK-Lysin / Saposin A-type domain / Saposin / Saposin A-type domain / Saposin A-type domain profile. / Saposin/surfactant protein-B A-type DOMAIN / Saposin-like type B, region 1 / Saposin-like type B, region 1 / Saposin B type, region 2 / Saposin-like type B, region 2 / Saposin (B) Domains / Saposin B type domain / Saposin-like / Saposin B type domain profile. / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
1,2-Distearoyl-sn-glycerophosphoethanolamine / Prosaposin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsAhn, 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
DepositionNov 8, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 7, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 2.0Jun 30, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_distant_solvent_atoms / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_comp_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_unobs_or_zero_occ_atoms.auth_comp_id / _pdbx_unobs_or_zero_occ_atoms.label_comp_id / _struct_ref_seq_dif.details / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 9BIOLOGICAL_UNIT: HOMODIMER
Remark 10OTHER DETAILS: METHIONINES SUBSTITUTED WITH SELENOMETHIONINE
Remark 600HETEROGEN 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 5WARNING 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).

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SAPOSIN B
B: SAPOSIN B
C: SAPOSIN B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1344
Polymers27,3863
Non-polymers7481
Water1,62190
1
A: SAPOSIN B
B: SAPOSIN B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0053
Polymers18,2572
Non-polymers7481
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4160 Å2
ΔGint-50 kcal/mol
Surface area8840 Å2
MethodPISA
2
C: SAPOSIN B

C: SAPOSIN B


Theoretical massNumber of molelcules
Total (without water)18,2572
Polymers18,2572
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Unit cell
Length a, b, c (Å)72.140, 72.140, 94.366
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein SAPOSIN B / Proactivator polypeptide / Sap-B / Sphingolipid activator protein 1 / SAP-1 / Cerebroside sulfate ...Proactivator polypeptide / Sap-B / Sphingolipid activator protein 1 / SAP-1 / Cerebroside sulfate activator / CSAct / CS-Act / Sulfatide/GM1 activator / GALACTOSYLCERBROSIDE ACTIVATOR


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 / 1,2-Distearoyl-sn-glycerophosphoethanolamine / 3-SN-PHOSPHATIDYLETHANOLAMINE / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE / Phosphatidylethanolamine


Mass: 748.065 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C41H82NO8P / Comment: phospholipid*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 90 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.68 Å3/Da / Density % sol: 54 %
Crystal growTemperature: 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
IDConc.Common nameCrystal-IDSol-IDDetails
130 mg/mlprotein1drop
216 %PEG33501reservoir
30.2 Mmagnesium acetate1reservoir
40.1 Msodium cacodylate1reservoirpH5.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 0.9789, 0.9793
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 21, 2000
RadiationProtocol: MAD, SE-MET / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97891
20.97931
ReflectionResolution: 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 shellResolution: 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

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SnBphasing
SHARPphasing
DMmodel building
CNS1.1refinement
CCP4(SCALA)data scaling
RefinementMethod 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
RfactorNum. reflection% reflectionSelection details
Rfree0.262 729 5 %RANDOM
Rwork0.222 ---
obs0.222 14613 98.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.3682 Å2 / ksol: 0.321762 e/Å3
Displacement parametersBiso mean: 45.8 Å2
Baniso -1Baniso -2Baniso -3
1--3.05 Å21.75 Å20 Å2
2---3.05 Å20 Å2
3---6.11 Å2
Refine analyzeLuzzati coordinate error free: 0.31 Å / Luzzati sigma a free: 0.22 Å
Refinement stepCycle: LAST / Resolution: 2.2→19.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1819 0 46 90 1955
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d18.3
X-RAY DIFFRACTIONc_improper_angle_d0.82
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.291 110 5 %
Rwork0.235 2096 -
obs--90.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3PEH.PARAMPEH.TOP
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 20 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0077
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg18.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.82

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