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- PDB-2gtg: Crystal Structure of Human Saposin C -

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Basic information

Entry
Database: PDB / ID: 2gtg
TitleCrystal Structure of Human Saposin C
ComponentsProactivator polypeptide
KeywordsLIPID BINDING PROTEIN / saposin / sphingolipid activator protein / lipid-binding protein
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: 2.4 Å
AuthorsPrive, G.G. / Ahn, V.E.
CitationJournal: Protein Sci. / Year: 2006
Title: Crystal structures of saposins A and C.
Authors: Ahn, V.E. / Leyko, P. / Alattia, J.R. / Chen, L. / Prive, G.G.
History
DepositionApr 28, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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)9,3061
Polymers9,3061
Non-polymers00
Water21612
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.204, 53.204, 52.460
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein Proactivator polypeptide


Mass: 9305.688 Da / Num. of mol.: 1 / Fragment: saposin C, residues 311-391
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSAP / Plasmid: pET16 / Production host: Escherichia coli (E. coli) / Strain (production host): AD494(DE3) / References: UniProt: P07602
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 46.59 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG400, Calcium Chloride, Sodium Hepes, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 4, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.4→26 Å / Num. all: 3896 / Num. obs: 3896 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 15.2 % / Rmerge(I) obs: 0.06
Reflection shellResolution: 2.4→2.48 Å / Rmerge(I) obs: 0.25 / % possible all: 74.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1M12

1m12


Resolution: 2.4→20 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.902 / SU B: 24.477 / SU ML: 0.263 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.743 / ESU R Free: 0.338 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.28257 465 14.2 %RANDOM
Rwork0.21083 ---
all0.22 2812 --
obs0.22136 2812 97.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 75.575 Å2
Baniso -1Baniso -2Baniso -3
1-1.69 Å20.85 Å20 Å2
2--1.69 Å20 Å2
3----2.54 Å2
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms609 0 0 12 621
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.022619
X-RAY DIFFRACTIONr_angle_refined_deg1.7292.018837
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.751577
X-RAY DIFFRACTIONr_dihedral_angle_2_deg49.64427.91724
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.08115126
X-RAY DIFFRACTIONr_chiral_restr0.1140.2103
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02432
X-RAY DIFFRACTIONr_nbd_refined0.250.2307
X-RAY DIFFRACTIONr_nbtor_refined0.3040.2446
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2240.220
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3440.221
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1360.23
X-RAY DIFFRACTIONr_mcbond_it0.9091.5406
X-RAY DIFFRACTIONr_mcangle_it1.3382640
X-RAY DIFFRACTIONr_scbond_it2.1053240
X-RAY DIFFRACTIONr_scangle_it3.2494.5197
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.399 31 -
Rwork0.239 173 -
obs--87.55 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
18.41930.4445-3.56467.6155-0.424313.18760.06150.2572-0.5755-0.308-0.04670.03451.4329-0.4038-0.0147-0.23180.1085-0.051-0.408-0.07240.033.78619.257-1.617
24.99450.0702-1.45446.58392.689816.816-0.109-0.2966-0.40940.21520.4568-0.86562.40411.8024-0.34780.06290.4731-0.0423-0.1267-0.03720.149914.59116.38-0.439
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 224 - 24
2X-RAY DIFFRACTION1AA55 - 7957 - 81
3X-RAY DIFFRACTION2AA23 - 5425 - 56

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