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- PDB-7p4t: Tetrameric structure of murine SapA -

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Basic information

Entry
Database: PDB / ID: 7p4t
TitleTetrameric structure of murine SapA
ComponentsSaposin-A
KeywordsLIPID BINDING PROTEIN / Saposin / disulfide / lipid transfer
Function / homology
Function and homology information


corneocyte development / membrane lipid metabolic process / glycolipid metabolic process / glucosylceramide metabolic process / inclusion body assembly / walking behavior / cornified envelope assembly / Glycosphingolipid catabolism / lipid antigen binding / galactosylceramide catabolic process ...corneocyte development / membrane lipid metabolic process / glycolipid metabolic process / glucosylceramide metabolic process / inclusion body assembly / walking behavior / cornified envelope assembly / Glycosphingolipid catabolism / lipid antigen binding / galactosylceramide catabolic process / micturition / Peptide ligand-binding receptors / cerebellar Purkinje cell differentiation / lysosomal protein catabolic process / ceramide metabolic process / G alpha (i) signalling events / Platelet degranulation / NK T cell differentiation / sphingolipid metabolic process / prostate gland growth / epithelial cell differentiation involved in prostate gland development / nervous system process / aggresome / lysosomal transport / : / cochlea development / antigen processing and presentation / regulation of MAPK cascade / neuromuscular process controlling balance / regulation of lipid metabolic process / protein secretion / developmental growth / myelination / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / Neutrophil degranulation / G protein-coupled receptor binding / sensory perception of sound / intracellular protein transport / cellular response to reactive oxygen species / late endosome / gene expression / protease binding / positive regulation of MAPK cascade / lysosome / mitochondrion / extracellular space / extracellular region / identical protein binding / cytoplasm
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
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.17 Å
AuthorsShamin, M. / Deane, J.E.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
CitationJournal: Contact / Year: 2021
Title: A Tetrameric Assembly of Saposin A: Increasing Structural Diversity in Lipid Transfer Proteins.
Authors: Shamin, M. / Spratley, S.J. / Graham, S.C. / Deane, J.E.
History
DepositionJul 13, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 25, 2022Provider: repository / Type: Initial release
Revision 1.1May 17, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_volume ..._citation.country / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Saposin-A
B: Saposin-A
C: Saposin-A
D: Saposin-A


Theoretical massNumber of molelcules
Total (without water)36,4944
Polymers36,4944
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.489, 48.489, 314.359
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Space group name HallP65
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: -x,-y,z+1/2

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Components

#1: Protein
Saposin-A


Mass: 9123.395 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Psap, Sgp1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q61207

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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: 2.92 Å3/Da / Density % sol: 57.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 23.25% (w/v) PEG 3350, 0.1 M Bis-Tris pH 5.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.17→52.4 Å / Num. obs: 5576 / % possible obs: 91.8 % / Redundancy: 10.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.178 / Rpim(I) all: 0.059 / Net I/σ(I): 5.5
Reflection shellResolution: 3.17→3.42 Å / Mean I/σ(I) obs: 1.1 / Num. unique obs: 372 / Rpim(I) all: 0.585

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Processing

Software
NameVersionClassification
DIALSdata collection
autoPROCdata scaling
PHASERphasing
PHENIX1.14_3260refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DDJ

4ddj


Resolution: 3.17→52.4 Å / Cross valid method: FREE R-VALUE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.304 --
Rwork0.272 --
obs-5571 79.1 %
Displacement parametersBiso mean: 113.05 Å2
Refinement stepCycle: LAST / Resolution: 3.17→52.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2432 0 0 0 2432
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00342464
X-RAY DIFFRACTIONf_angle_d0.77363344
X-RAY DIFFRACTIONf_chiral_restr0.0458408
X-RAY DIFFRACTIONf_plane_restr0.0047424
X-RAY DIFFRACTIONf_dihedral_angle_d13.68671564

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