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- PDB-2qyp: Orthorhombic Crystal Structure of Human Saposin C Dimer in Open C... -

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Basic information

Entry
Database: PDB / ID: 2qyp
TitleOrthorhombic Crystal Structure of Human Saposin C Dimer in Open Conformation
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 / 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 metabolism / lysosomal transport / azurophil granule membrane / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / enzyme activator activity / regulation of lipid metabolic process / Peptide ligand-binding receptors / lysosomal lumen / regulation of autophagy / phospholipid binding / G alpha (i) signalling events / late endosome / Platelet degranulation / scaffold protein binding / collagen-containing extracellular matrix / protease binding / lysosomal membrane / lysosome / 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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.45 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 15, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Proactivator polypeptide
B: Proactivator polypeptide


Theoretical massNumber of molelcules
Total (without water)20,7582
Polymers20,7582
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.008, 88.904, 93.465
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: 10378.861 Da / Num. of mol.: 2 / Fragment: Saposin-C Domain
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

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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: 2.85 Å3/Da / Density % sol: 56.88 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 20 mM NaAcetate, 200 mM ammonium sulfate, 30% (v/v) pentaerythriol ethoxylate 15/4, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.54179 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 22, 2003 / Details: Osmic MaxFlux
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 2.45→32.2 Å / Num. all: 8971 / Num. obs: 8971 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 3 / Redundancy: 2.89 % / Biso Wilson estimate: 76.9 Å2 / Rsym value: 0.055 / Net I/σ(I): 17
Reflection shellResolution: 2.45→2.54 Å / Mean I/σ(I) obs: 2.1 / Num. unique all: 898 / Rsym value: 0.46 / % possible all: 99.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3 Å32.21 Å
Translation3 Å32.21 Å

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Processing

Software
NameVersionClassificationNB
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3data extraction
MAR345dtbdata collection
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.45→28.5 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.91 / SU B: 9.484 / SU ML: 0.219 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / ESU R: 0.386 / ESU R Free: 0.296 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29 548 4.9 %RANDOM
Rwork0.229 ---
obs0.232 7875 91.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 70.279 Å2
Baniso -1Baniso -2Baniso -3
1-0.41 Å20 Å20 Å2
2---0.04 Å20 Å2
3----0.38 Å2
Refinement stepCycle: LAST / Resolution: 2.45→28.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1242 0 0 0 1242
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221263
X-RAY DIFFRACTIONr_angle_refined_deg1.32.0161709
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5275157
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.99727.75549
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.86615254
X-RAY DIFFRACTIONr_chiral_restr0.0860.2210
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02884
X-RAY DIFFRACTIONr_nbd_refined0.2280.2569
X-RAY DIFFRACTIONr_nbtor_refined0.2980.2901
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.29
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2280.241
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2240.21
X-RAY DIFFRACTIONr_mcbond_it0.7871.5821
X-RAY DIFFRACTIONr_mcangle_it1.35421304
X-RAY DIFFRACTIONr_scbond_it1.8923490
X-RAY DIFFRACTIONr_scangle_it3.074.5405
LS refinement shellResolution: 2.45→2.54 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.29 390
Rwork0.229 548
all-582
obs-7875

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