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- PDB-2r1q: Crystal Structure of Iodinated Human Saposin D in Space Group C2221 -

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Basic information

Entry
Database: PDB / ID: 2r1q
TitleCrystal Structure of Iodinated Human Saposin D in Space Group C2221
ComponentsProactivator polypeptide
KeywordsLIPID BINDING PROTEIN / saposin / activator protein / sap / Alternative splicing / 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 / 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
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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
DepositionAug 23, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Proactivator polypeptide


Theoretical massNumber of molelcules
Total (without water)9,7801
Polymers9,7801
Non-polymers00
Water1086
1
A: Proactivator polypeptide

A: Proactivator polypeptide


Theoretical massNumber of molelcules
Total (without water)19,5602
Polymers19,5602
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
MethodPISA
Unit cell
Length a, b, c (Å)40.465, 74.879, 66.791
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Proactivator polypeptide


Mass: 9780.049 Da / Num. of mol.: 1
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2.59 Å3/Da / Density % sol: 52.45 %
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: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 1.12714 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 23, 2004 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12714 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 3670 / % possible obs: 98.7 % / Rmerge(I) obs: 0.104 / Χ2: 1.034 / Net I/σ(I): 12.3
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2% possible all
2.5-2.590.5463420.85897.7
2.59-2.690.4193631.06998.1
2.69-2.810.3223521.07897.5
2.81-2.960.2443511.0397.8
2.96-3.150.1843641.07798.1
3.15-3.390.1433681.06299.5
3.39-3.730.1133721.079100
3.73-4.260.0913731.03299.7
4.26-5.350.0773801.01799.2
5.35-200.0934051.02699.3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3data extraction
MAR345dtbdata collection
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→19.35 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.909 / SU B: 12.191 / SU ML: 0.252 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.491 / ESU R Free: 0.298 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.278 162 4.4 %RANDOM
Rwork0.248 ---
obs0.25 3657 98.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.44 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å20 Å20 Å2
2---0.26 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.5→19.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms609 0 0 8 617
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.022623
X-RAY DIFFRACTIONr_angle_refined_deg1.3892.027844
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.373577
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.03726.825
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.00615113
X-RAY DIFFRACTIONr_dihedral_angle_4_deg39.701151
X-RAY DIFFRACTIONr_chiral_restr0.10.295
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02458
X-RAY DIFFRACTIONr_nbd_refined0.2430.2286
X-RAY DIFFRACTIONr_nbtor_refined0.3130.2435
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1220.222
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2570.224
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3060.21
X-RAY DIFFRACTIONr_mcbond_it0.4471.5396
X-RAY DIFFRACTIONr_mcangle_it0.862631
X-RAY DIFFRACTIONr_scbond_it1.4463253
X-RAY DIFFRACTIONr_scangle_it2.1384.5213
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 12 -
Rwork0.354 239 -
all-251 -
obs--98.82 %

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