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- PDB-9i63: Synthetic Human Saposin D glycoprotein -

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Basic information

Entry
Database: PDB / ID: 9i63
TitleSynthetic Human Saposin D glycoprotein
ComponentsProsaposin
KeywordsLIPID BINDING PROTEIN / glycoprotein / ligation / lipid metabolism / n-glycan
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 / azurophil granule membrane / lysosomal transport / regulation of lipid metabolic process / lysosomal lumen / enzyme activator activity / Peptide ligand-binding receptors / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / phospholipid binding / late endosome / Platelet degranulation / protease binding / scaffold protein binding / : / G alpha (i) signalling events / lysosome / regulation of autophagy / 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 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, chordata / 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.
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsWeyand, M. / Unverzagt, C.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)UN63/5-1 Germany
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2017
Title: Synthetic Glycoforms Reveal Carbohydrate-Dependent Bioactivity of Human Saposin D.
Authors: Graf, C.G.F. / Schulz, C. / Schmalzlein, M. / Heinlein, C. / Monnich, M. / Perkams, L. / Puttner, M. / Boos, I. / Hessefort, M. / Lombana Sanchez, J.N. / Weyand, M. / Steegborn, C. / ...Authors: Graf, C.G.F. / Schulz, C. / Schmalzlein, M. / Heinlein, C. / Monnich, M. / Perkams, L. / Puttner, M. / Boos, I. / Hessefort, M. / Lombana Sanchez, J.N. / Weyand, M. / Steegborn, C. / Breiden, B. / Ross, K. / Schwarzmann, G. / Sandhoff, K. / Unverzagt, C.
History
DepositionJan 29, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 9, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Prosaposin
B: Prosaposin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3313
Polymers18,2352
Non-polymers961
Water3,837213
1
A: Prosaposin


Theoretical massNumber of molelcules
Total (without water)9,1181
Polymers9,1181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Prosaposin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,2142
Polymers9,1181
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.440, 65.680, 42.470
Angle α, β, γ (deg.)90.000, 114.498, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Prosaposin / Proactivator polypeptide


Mass: 9117.519 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P07602
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.81 Å3/Da / Density % sol: 56.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 2.4 M (NH4)2SO4, 0.2 M NH4OAc, 20 mM Tris pH 7.5 / PH range: 7.0-7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918007 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 5, 2015 / Details: Sagitally bended Si111-crystal
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918007 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 23455 / % possible obs: 96 % / Redundancy: 3.12 % / Biso Wilson estimate: 25.765 Å2 / CC1/2: 0.987 / Rmerge(I) obs: 0.091 / Rrim(I) all: 0.105 / Net I/σ(I): 13.73
Reflection shellResolution: 1.65→1.67 Å / Redundancy: 2.04 % / Rmerge(I) obs: 0.423 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 659 / CC1/2: 0.695 / Rrim(I) all: 0.569 / % possible all: 78.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
XDSdata reduction
XSCALEdata scaling
PHASER2.5.7phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→36.799 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.941 / SU B: 4.988 / SU ML: 0.072 / Cross valid method: FREE R-VALUE / ESU R: 0.113 / ESU R Free: 0.089
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2011 1173 5.001 %
Rwork0.1614 22282 -
all0.163 --
obs-23455 96.245 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 17.721 Å2
Baniso -1Baniso -2Baniso -3
1-3.09 Å2-0 Å20.587 Å2
2---0.631 Å20 Å2
3----2.115 Å2
Refinement stepCycle: LAST / Resolution: 1.65→36.799 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1203 0 5 213 1421
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0121327
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161289
X-RAY DIFFRACTIONr_angle_refined_deg2.0131.8461823
X-RAY DIFFRACTIONr_angle_other_deg0.6921.7363017
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8885180
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3.28552
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.68810239
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.2341058
X-RAY DIFFRACTIONr_chiral_restr0.1040.2210
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021513
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02259
X-RAY DIFFRACTIONr_nbd_refined0.2420.2335
X-RAY DIFFRACTIONr_symmetry_nbd_other0.190.21124
X-RAY DIFFRACTIONr_nbtor_refined0.1890.2653
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0740.2665
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2122
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0490.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0950.27
X-RAY DIFFRACTIONr_nbd_other0.2040.236
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1220.210
X-RAY DIFFRACTIONr_mcbond_it4.8931.767653
X-RAY DIFFRACTIONr_mcbond_other4.8591.766653
X-RAY DIFFRACTIONr_mcangle_it7.2393.179821
X-RAY DIFFRACTIONr_mcangle_other7.2553.182822
X-RAY DIFFRACTIONr_scbond_it6.4692.019674
X-RAY DIFFRACTIONr_scbond_other6.3482.01671
X-RAY DIFFRACTIONr_scangle_it9.5243.622989
X-RAY DIFFRACTIONr_scangle_other9.3623.603984
X-RAY DIFFRACTIONr_lrange_it14.99920.7441623
X-RAY DIFFRACTIONr_lrange_other13.64318.2941570
X-RAY DIFFRACTIONr_rigid_bond_restr5.60332616
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.65-1.6930.3710.28213550.28317870.9720.97979.79850.235
1.693-1.7390.263770.25414690.25417410.9770.98388.79950.202
1.739-1.7890.251830.21715660.21916970.9850.98897.17150.163
1.789-1.8440.269820.19615580.216620.9750.98898.67630.144
1.844-1.9050.246780.17914750.18215780.9770.98898.41570.132
1.905-1.9710.188760.1614500.16215430.9810.9998.89820.116
1.971-2.0460.237740.14914060.15315130.9650.9997.81890.118
2.046-2.1290.19720.14713650.14914540.9830.99198.83080.123
2.129-2.2230.209680.14812940.15113680.9710.9999.56140.129
2.223-2.3310.178650.14712440.14813110.9870.9999.84740.128
2.331-2.4570.158630.13611890.13712580.9850.9999.5230.122
2.457-2.6050.174590.13811230.13911930.9850.99199.07790.126
2.605-2.7840.186550.14310510.14611200.9820.98798.750.138
2.784-3.0060.181530.1519970.15210580.9850.98699.24390.149
3.006-3.290.185470.1418890.1439540.9790.98998.11320.144
3.29-3.6750.194430.1478220.1498850.9750.98897.74010.16
3.675-4.2360.161360.1386960.1397560.9850.98996.82540.152
4.236-5.1710.219320.1565930.1596670.9740.98993.70310.181
5.171-7.2420.23250.2594750.2585190.970.97496.33910.292
7.242-36.7990.279140.2132650.2153050.9480.97991.47540.256

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