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- PDB-2r0r: Crystal Structure of Human Saposin D variant SapD K9E -

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Basic information

Entry
Database: PDB / ID: 2r0r
TitleCrystal Structure of Human Saposin D variant SapD K9E
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 / protease binding / collagen-containing extracellular matrix / 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, 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 / molecular replacement / Resolution: 2.5 Å
AuthorsRossmann, M. / Saenger, W. / Maier, T.
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 21, 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
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)19,4043
Polymers19,3082
Non-polymers961
Water1,892105
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.434, 66.029, 42.467
Angle α, β, γ (deg.)90.00, 114.83, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Proactivator polypeptide


Mass: 9654.087 Da / Num. of mol.: 2 / Mutation: K9E
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


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.: 105 / Source method: isolated from a natural source / Formula: H2O
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: 2.66 Å3/Da / Density % sol: 53.84 %
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: 0.954 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 28, 2005 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionAv σ(I) over netI: 14.7 / Number: 21402 / Rmerge(I) obs: 0.075 / Χ2: 1.03 / D res high: 2.5 Å / D res low: 30 Å / Num. obs: 6704 / % possible obs: 94.6
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squared
5.383098.810.0540.752
4.275.3899.910.0610.765
3.734.2710010.0681.058
3.393.7399.710.081.058
3.153.3999.910.0911.057
2.963.1599.910.110.981
2.822.9698.910.1251.155
2.692.8292.710.131.201
2.592.6983.710.1321.355
2.52.5971.610.1181.433
ReflectionResolution: 2.5→30 Å / Num. obs: 6704 / % possible obs: 94.6 % / Redundancy: 3.2 % / Biso Wilson estimate: 43.8 Å2 / Rmerge(I) obs: 0.075 / Χ2: 1.033 / Net I/σ(I): 14.7
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2% possible all
2.5-2.590.1184861.43371.6
2.59-2.690.1326051.35583.7
2.69-2.820.136501.20192.7
2.82-2.960.1256921.15598.9
2.96-3.150.117020.98199.9
3.15-3.390.0917121.05799.9
3.39-3.730.087111.05899.7
3.73-4.270.0687081.058100
4.27-5.380.0617110.76599.9
5.38-300.0547270.75298.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3 Å25.08 Å
Translation3 Å25.08 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3data extraction
MAR345dtbdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→25.07 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.854 / SU B: 10.53 / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.598 / ESU R Free: 0.338 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.287 313 4.7 %RANDOM
Rwork0.21 ---
obs0.214 6693 94.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.726 Å2
Baniso -1Baniso -2Baniso -3
1--1.44 Å20 Å20.69 Å2
2--0.07 Å20 Å2
3---1.94 Å2
Refinement stepCycle: LAST / Resolution: 2.5→25.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1220 0 5 105 1330
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221243
X-RAY DIFFRACTIONr_angle_refined_deg1.1972.011685
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1015153
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.87826.66754
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.18215224
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.7152
X-RAY DIFFRACTIONr_chiral_restr0.0850.2189
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02918
X-RAY DIFFRACTIONr_nbd_refined0.2180.2620
X-RAY DIFFRACTIONr_nbtor_refined0.3010.2864
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.120.274
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1780.238
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1220.26
X-RAY DIFFRACTIONr_mcbond_it0.4581.5811
X-RAY DIFFRACTIONr_mcangle_it0.79121255
X-RAY DIFFRACTIONr_scbond_it0.9123496
X-RAY DIFFRACTIONr_scangle_it1.4744.5430
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 13 -
Rwork0.264 326 -
all-339 -
obs--68.48 %

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