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- PDB-9axg: Human saposin B in the presence of globotriaosylceramide-NBD -

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Basic information

Entry
Database: PDB / ID: 9axg
TitleHuman saposin B in the presence of globotriaosylceramide-NBD
ComponentsSaposin-B
KeywordsLIPID BINDING PROTEIN / Saposin / Saposin B / SapB / Fabry disease / Lysosomal / Activator protein / Globotriaosylceramide / Gb3 / Nitrobenzoxadiazole / NBD
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 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, chordata / 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.
Similarity search - Domain/homology
MALONATE ION / Prosaposin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.68 Å
AuthorsSawyer, T.K. / Garman, S.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)5R01DK076877 United States
CitationJournal: Biorxiv / Year: 2024
Title: Human Saposin B Ligand Binding and Presentation to alpha-Galactosidase A.
Authors: Sawyer, T.K. / Aral, E. / Staros, J.V. / Bobst, C.E. / Garman, S.C.
History
DepositionMar 6, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Apr 24, 2024Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Saposin-B
B: Saposin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2973
Polymers18,1952
Non-polymers1021
Water543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1740 Å2
ΔGint-17 kcal/mol
Surface area9820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.908, 66.908, 87.181
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number172
Space group name H-MP64
Space group name HallP64
Symmetry operation#1: x,y,z
#2: x-y,x,z+2/3
#3: y,-x+y,z+1/3
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z

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Components

#1: Protein Saposin-B / Cerebroside sulfate activator / CSAct / Dispersin / Sphingolipid activator protein 1 / SAP-1 / ...Cerebroside sulfate activator / CSAct / Dispersin / Sphingolipid activator protein 1 / SAP-1 / Sulfatide/GM1 activator


Mass: 9097.452 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: N-terminal GAS linker from purification. Fragment corresponds to residues 195-273 of canonical isoform P07602-1.
Source: (gene. exp.) Homo sapiens (human) / Gene: PSAP, GLBA, SAP1 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): Shuffle Express / References: UniProt: P07602
#2: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.2 Å3/Da / Density % sol: 61.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 500 nL of protein-lipid complex (0.82 mM SapB plus 0.87 mM Gb3-NBD) was mixed with 250 nL of reservoir solution (3.1-3.3 M malonate pH 5) and equilibrated against 70 uL reservoirs at 20 C.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.68→34.83 Å / Num. obs: 6246 / % possible obs: 99.74 % / Redundancy: 9.7 % / Biso Wilson estimate: 82.42 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.0432 / Net I/σ(I): 27.07
Reflection shellResolution: 2.68→2.776 Å / Rmerge(I) obs: 0.368 / Mean I/σ(I) obs: 1.51 / Num. unique obs: 609 / CC1/2: 0.963 / % possible all: 100

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX1.20.1_4487refinement
xia2data reduction
xia2data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.68→34.83 Å / SU ML: 0.3725 / Cross valid method: FREE R-VALUE / σ(F): 1.43 / Phase error: 35.334
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2868 619 9.92 %
Rwork0.2436 5622 -
obs0.2478 6241 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 93.94 Å2
Refinement stepCycle: LAST / Resolution: 2.68→34.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1157 0 7 3 1167
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00751175
X-RAY DIFFRACTIONf_angle_d0.96211587
X-RAY DIFFRACTIONf_chiral_restr0.0501187
X-RAY DIFFRACTIONf_plane_restr0.007212
X-RAY DIFFRACTIONf_dihedral_angle_d7.6974165
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.68-2.950.341380.28331404X-RAY DIFFRACTION99.87
2.95-3.380.33221500.30091405X-RAY DIFFRACTION99.94
3.38-4.250.34671780.24441387X-RAY DIFFRACTION100
4.26-34.830.23821530.22591426X-RAY DIFFRACTION99.37
Refinement TLS params.Method: refined / Origin x: -12.6700161823 Å / Origin y: -13.4675851744 Å / Origin z: -6.08609887148 Å
111213212223313233
T0.444623476407 Å2-0.072959483157 Å20.040769979989 Å2-0.418053013136 Å20.0238541781803 Å2--0.61672679776 Å2
L3.70639166176 °2-0.158078824879 °2-0.9990629089 °2-3.87121425613 °20.86770809215 °2--7.38226649643 °2
S-0.0478017521491 Å °-0.0651837804343 Å °0.209388056327 Å °0.0559481239884 Å °0.00203837827018 Å °-0.14693341042 Å °-0.286076675292 Å °-0.0621476806564 Å °0.037471274199 Å °
Refinement TLS groupSelection details: all

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