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- PDB-2z9a: Crystal Structure of Human Saposin C Dimer in Open Conformation -

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Basic information

Entry
Database: PDB / ID: 2z9a
TitleCrystal Structure of Human Saposin C Dimer in Open Conformation
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 / epithelial cell differentiation involved in prostate gland development / sphingolipid metabolic process ...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 / epithelial cell differentiation involved in prostate gland development / sphingolipid metabolic process / 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 / SYNCHROTRON / 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
DepositionSep 18, 2007Deposition site: PDBJ / Processing site: RCSB
Revision 1.0Apr 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Aug 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4834
Polymers20,2992
Non-polymers1842
Water52229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.990, 48.990, 155.570
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Proactivator polypeptide


Mass: 10149.628 Da / Num. of mol.: 2
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 29 / 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: 2.3 Å3/Da / Density % sol: 46.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 20 mM NaAcetate, 240 mM magnesium sulfate, 41% (v/v) pentaerythriol ethoxylate 15/4, pH 4.0, vapor diffusion, sitting drop, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 8, 2004 / Details: toroidal mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.5→25 Å / Num. obs: 7088 / % possible obs: 99.5 % / Biso Wilson estimate: 47.985 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 18.83
Reflection shellResolution: 2.5→2.6 Å / Rmerge(I) obs: 0.567 / Mean I/σ(I) obs: 6.3 / Num. measured obs: 10366 / Num. unique all: 10030 / Num. unique obs: 760 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACT3data extraction
ADSCQuantumdata collection
XDSdata reduction
MOLREPphasing
RefinementStarting model: pdb entry 2gtg

2gtg


Resolution: 2.5→25 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.913 / SU B: 9.643 / SU ML: 0.22 / Cross valid method: THROUGHOUT / ESU R: 0.515 / ESU R Free: 0.296 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.271 335 4.7 %RANDOM
Rwork0.239 ---
obs0.24 7087 99.68 %-
all-10030 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.373 Å2
Baniso -1Baniso -2Baniso -3
1-2.56 Å20 Å20 Å2
2--2.56 Å20 Å2
3----5.11 Å2
Refinement stepCycle: LAST / Resolution: 2.5→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1212 0 12 29 1253
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221240
X-RAY DIFFRACTIONr_angle_refined_deg1.3322.0211672
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7845153
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.38927.91748
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.15515251
X-RAY DIFFRACTIONr_chiral_restr0.0890.2205
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02852
X-RAY DIFFRACTIONr_nbd_refined0.2110.2548
X-RAY DIFFRACTIONr_nbtor_refined0.3010.2854
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.244
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2220.231
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2020.25
X-RAY DIFFRACTIONr_mcbond_it0.6361.5800
X-RAY DIFFRACTIONr_mcangle_it1.15421268
X-RAY DIFFRACTIONr_scbond_it1.6823487
X-RAY DIFFRACTIONr_scangle_it2.7734.5404
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 18 -
Rwork0.245 489 -
all-507 -
obs--100 %

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