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- PDB-5u85: Murine saposin-D (SapD), open conformation -

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Basic information

Entry
Database: PDB / ID: 5u85
TitleMurine saposin-D (SapD), open conformation
ComponentsSaposin-D
KeywordsLIPID BINDING PROTEIN / saposin
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-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 speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.65 Å
AuthorsGebai, A. / Gorelik, A. / Illes, K. / Nagar, B.
CitationJournal: J. Struct. Biol. / Year: 2018
Title: Crystal structure of saposin D in an open conformation.
Authors: Gebai, A. / Gorelik, A. / Nagar, B.
History
DepositionDec 13, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 1, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 10, 2018Group: Data collection / Database references / Structure summary
Category: citation / entity
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _entity.formula_weight
Revision 1.3May 22, 2019Group: Data collection / Structure summary / Category: entity / struct_keywords
Item: _entity.formula_weight / _struct_keywords.pdbx_keywords / _struct_keywords.text

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)18,5432
Polymers18,5432
Non-polymers00
Water3,567198
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2990 Å2
ΔGint-39 kcal/mol
Surface area8740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.650, 43.163, 88.822
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsDimer as determined by gel filtration

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Components

#1: Protein Saposin-D / Sulfated glycoprotein 1 / SGP-1


Mass: 9271.682 Da / Num. of mol.: 2 / Fragment: Saposin B-type 4 domain, residues 438-519
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Psap, Sgp1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q61207
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / 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: 2.28 Å3/Da / Density % sol: 46.17 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: sodium citrate PEG 4000 isopropanol / PH range: 5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Nov 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 19863 / % possible obs: 100 % / Redundancy: 7.1 % / Net I/σ(I): 33.2

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
HKL-2000data reduction
HKL-2000data scaling
ACORNphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.65→38.822 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.21
RfactorNum. reflection% reflection
Rfree0.1857 1430 4.99 %
Rwork0.1662 --
obs0.1672 18902 76.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.65→38.822 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1216 0 0 198 1414
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031293
X-RAY DIFFRACTIONf_angle_d0.6651761
X-RAY DIFFRACTIONf_dihedral_angle_d10.975830
X-RAY DIFFRACTIONf_chiral_restr0.035200
X-RAY DIFFRACTIONf_plane_restr0.004225
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.7090.242640.22931347X-RAY DIFFRACTION38
1.709-1.77740.2425810.21511536X-RAY DIFFRACTION44
1.7774-1.85830.2051090.21011926X-RAY DIFFRACTION55
1.8583-1.95630.21481190.20512323X-RAY DIFFRACTION65
1.9563-2.07890.20171410.16662773X-RAY DIFFRACTION78
2.0789-2.23940.19011720.15353216X-RAY DIFFRACTION92
2.2394-2.46470.17671860.14653520X-RAY DIFFRACTION99
2.4647-2.82120.19051880.15583554X-RAY DIFFRACTION100
2.8212-3.55410.16931870.16213527X-RAY DIFFRACTION100
3.5541-38.83260.17821830.16793492X-RAY DIFFRACTION99
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)
10.00090.0001-0.00060.00120.00030.00060.0036-0.00310.00520.0029-0.0030.00780.00540.03090-0.06410.04310.0120.0169-0.02390.0208-13.09286.1161-18.132
2-0.00020.001-0.00180.0008-0.00140.00070.0058-0.0077-0.0220.01570.0094-0.0086-0.0164-0.0156-00.02460.01040.05460.018-0.01130.0308-35.258914.903-10.6354
3-0.0004-0.0024-0.0022-0.0024-0.0029-0.00110.027-0.01030.00990.01910.0277-0.0249-0.0067-0.0295-0-0.0026-0.02370.0797-0.09520.1912-0.1619-30.520922.4169-13.9518
40.0010.00020.00050.0005-0.000100.00780.00620.0013-0.00470.0147-0.019400.0046-00.0484-0.0375-0.08460.0527-0.04730.1336-6.426712.4299-12.999
50.00120.00170.00210.00080.00120.00060.0022-0.0208-0.00040.00010.0045-0.004-0.0150.0039-00.08020.02850.00780.0589-0.00270.0362-28.14820.381-3.584
60.00110.00040.0015-0.00060.00230.00050.008-0.0014-0.00820.00160.0028-0.00540.0160.0008-00.00210.00830.030.0297-0.0863-0.0694-18.9505-1.3563-11.7854
70.00290.00090.00090.00040.00010.0009-0.0008-0.0023-0.0086-0.0030.0109-0.01380.01180.009800.0740.0201-0.06130.0542-0.01840.014-11.32354.6712-7.7909
80.00050.0005-0.00010.0004-0.00010.0002-0.00660.00470.01140.0027-0.0033-0.002-0.00110.004-00.1638-0.0454-0.01120.05030.01720.1088-21.884927.4608-9.5897
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 21 )
2X-RAY DIFFRACTION2chain 'A' and (resid 22 through 42 )
3X-RAY DIFFRACTION3chain 'A' and (resid 43 through 65 )
4X-RAY DIFFRACTION4chain 'A' and (resid 66 through 80 )
5X-RAY DIFFRACTION5chain 'B' and (resid 3 through 21 )
6X-RAY DIFFRACTION6chain 'B' and (resid 22 through 42 )
7X-RAY DIFFRACTION7chain 'B' and (resid 43 through 65 )
8X-RAY DIFFRACTION8chain 'B' and (resid 66 through 79 )

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