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- PDB-2rb3: Crystal Structure of Human Saposin D -

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Basic information

Entry
Database: PDB / ID: 2rb3
TitleCrystal Structure of Human Saposin D
ComponentsProactivator polypeptide
KeywordsLIPID BINDING PROTEIN / saposin / activator protein / sap / Disease mutation / Gaucher disease / Glycoprotein / GM2-gangliosidosis / Lipid metabolism / Lysosome / Metachromatic leukodystrophy / 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
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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsMaier, T. / Rossman, M. / Saenger, W.
CitationJournal: Structure / Year: 2008
Title: Crystal structures of human saposins C and d: implications for lipid recognition and membrane interactions.
Authors: Rossmann, M. / Schultz-Heienbrok, R. / Behlke, J. / Remmel, N. / Alings, C. / Sandhoff, K. / Saenger, W. / Maier, T.
History
DepositionSep 18, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Proactivator polypeptide
B: Proactivator polypeptide
C: Proactivator polypeptide
D: Proactivator polypeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0899
Polymers38,6174
Non-polymers4725
Water6,864381
1
A: Proactivator polypeptide
D: Proactivator polypeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5935
Polymers19,3082
Non-polymers2843
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Proactivator polypeptide
C: Proactivator polypeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4964
Polymers19,3082
Non-polymers1882
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.154, 41.088, 65.929
Angle α, β, γ (deg.)89.96, 80.84, 71.49
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Proactivator polypeptide


Mass: 9654.152 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSAP, GLBA, SAP1 / Plasmid: pPIC9K / Production host: Pichia pastoris (fungus) / Strain (production host): GS115 / References: UniProt: P07602
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 381 / 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: 2.63 Å3/Da / Density % sol: 53.29 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.9
Details: 100 mM BisTris, 2.3 M ammonium sulfate, 100 mM urea, pH 5.9, vapor diffusion, hanging drop, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: OTHER / Wavelength: 1.54179 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 6, 2002 / Details: mirrors
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. obs: 21734 / % possible obs: 94.5 % / Biso Wilson estimate: 39 Å2 / Rmerge(I) obs: 0.051 / Χ2: 1.045 / Net I/σ(I): 22
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.1-2.180.18521091.057191.7
2.18-2.260.15921311.019192.8
2.26-2.370.12821521.015192.9
2.37-2.490.10721351.094193.5
2.49-2.650.09221591.058194
2.65-2.850.07721831.062195.1
2.85-3.140.05921991.016195.3
3.14-3.590.04521931.016195.8
3.59-4.520.03822351.046196.8
4.52-300.02822381.07197.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3data extraction
MAR345dtbdata collection
AMoREphasing
RefinementStarting model: pdb entry 2r0r

2r0r


Resolution: 2.1→21.67 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.894 / SU B: 5.571 / SU ML: 0.152 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.262 / ESU R Free: 0.225 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.274 1100 5.1 %RANDOM
Rwork0.211 ---
obs0.214 21733 94.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.617 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20.02 Å2-0.02 Å2
2--0.02 Å2-0.09 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 2.1→21.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2450 0 27 381 2858
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222596
X-RAY DIFFRACTIONr_angle_refined_deg1.2472.0173523
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4415325
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.57126.636107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.96415475
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.067154
X-RAY DIFFRACTIONr_chiral_restr0.0870.2391
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021920
X-RAY DIFFRACTIONr_nbd_refined0.2020.21323
X-RAY DIFFRACTIONr_nbtor_refined0.2920.21808
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.2267
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1270.260
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1230.221
X-RAY DIFFRACTIONr_mcbond_it0.5511.51702
X-RAY DIFFRACTIONr_mcangle_it0.91922632
X-RAY DIFFRACTIONr_scbond_it1.1331032
X-RAY DIFFRACTIONr_scangle_it1.794.5891
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.404 64 -
Rwork0.257 1509 -
all-1573 -
obs--91.45 %

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