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- PDB-1m12: NMR solution structure of human Saposin C -

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Basic information

Entry
Database: PDB / ID: 1m12
TitleNMR solution structure of human Saposin C
ComponentsSAPOSIN C
KeywordsMEMBRANE PROTEIN / disulfide bridges / alpha-helices
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)
MethodSOLUTION NMR / distance geometry, simulated annealing
Authorsde Alba, E. / Weiler, S. / Tjandra, N.
CitationJournal: Biochemistry / Year: 2003
Title: Solution structure of human saposin C: pH-dependent interaction with phospholipid vesicles.
Authors: de Alba, E. / Weiler, S. / Tjandra, N.
History
DepositionJun 17, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SAPOSIN C


Theoretical massNumber of molelcules
Total (without water)9,4251
Polymers9,4251
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 163structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein SAPOSIN C


Mass: 9424.898 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P07602

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1224D 13C/15N-separated NOESY
1334D 13C-separated NOESY
1433D 13C-separated TOCSY
152CBCA(CO)NH, HN(CA)CB
162experiments for residual dipolar coupling measurements
NMR detailsText: residual dipolar couplings measured in two different alignment media. Pf1 and fd phages

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Sample preparation

Details
Solution-IDContentsSolvent system
1U-15N90% H20, 10% D20
2U-15N, U-13C90% H20, 10% D20
3U-15N, U-13C100% D20
Sample conditionsIonic strength: ~10-20mM NaCl / pH: 6.8 / Pressure: ambient / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR
Components of the solutions
*PLUS
IDCrystal-ID
11
21
31
41

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DMXBrukerDMX8002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.5Brukercollection
NMRPipe2.1Delagioprocessing
PIPP4.2.8Garrettdata analysis
X-PLOR3.84Brungerrefinement
RefinementMethod: distance geometry, simulated annealing / Software ordinal: 1
Details: structures were calculated with: 1806 NOE-derived destance constriants (no intra-residue NOEs used), 28 hydrogen bonds, 135 dihedral restraints, 276 residual dipolar couplings. Residues 1-3 ...Details: structures were calculated with: 1806 NOE-derived destance constriants (no intra-residue NOEs used), 28 hydrogen bonds, 135 dihedral restraints, 276 residual dipolar couplings. Residues 1-3 and 79-84 are disordered. Superimposition of structures is from residues 4-78.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 163 / Conformers submitted total number: 20

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