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- PDB-4ddj: Crystal structure of saposin A in complex with lauryldimethylamin... -

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Basic information

Entry
Database: PDB / ID: 4ddj
TitleCrystal structure of saposin A in complex with lauryldimethylamine-N-oxide (LDAO)
ComponentsSaposin-A
KeywordsLIPID BINDING PROTEIN / saposin fold / sphingolipid activator protein / galactosylceramide / lauryldimethylamine-N-oxide / lipid / detergent / lysosome
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 / Glycosphingolipid catabolism ...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 / Glycosphingolipid catabolism / epithelial cell differentiation involved in prostate gland development / lysosomal transport / azurophil granule membrane / regulation of lipid metabolic process / enzyme activator activity / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / Peptide ligand-binding receptors / lysosomal lumen / 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 / SAD / Resolution: 1.9 Å
AuthorsPopovic, K. / Prive, G.G.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Structure of saposin A lipoprotein discs.
Authors: Popovic, K. / Holyoake, J. / Pomes, R. / Prive, G.G.
History
DepositionJan 18, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2012Group: Database references
Revision 1.2Mar 14, 2012Group: Database references
Revision 1.3Jan 29, 2020Group: Advisory / Database references / Derived calculations
Category: pdbx_distant_solvent_atoms / pdbx_struct_assembly ...pdbx_distant_solvent_atoms / pdbx_struct_assembly / pdbx_struct_assembly_gen / struct_ref_seq_dif
Item: _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Saposin-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,65021
Polymers9,0611
Non-polymers4,58820
Water1,17165
1
A: Saposin-A
hetero molecules

A: Saposin-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,29942
Polymers18,1232
Non-polymers9,17640
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Unit cell
Length a, b, c (Å)39.794, 39.794, 247.284
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Saposin-A / Protein A


Mass: 9061.495 Da / Num. of mol.: 1 / Fragment: UNP residues 60-140
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSAP, GLBA, SAP1 / Production host: Escherichia coli (E. coli) / References: UniProt: P07602
#2: Chemical
ChemComp-LDA / LAURYL DIMETHYLAMINE-N-OXIDE


Mass: 229.402 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C14H31NO / Comment: LDAO, detergent*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsALTHOUGH THE REAL SPACE R VALUE FOR SOME OF THE LDA RESIDUES ARE HIGH, THESE LDAO DETERGENT ...ALTHOUGH THE REAL SPACE R VALUE FOR SOME OF THE LDA RESIDUES ARE HIGH, THESE LDAO DETERGENT MOLECULES (RESIDUE NAME IS LDA) ARE PART OF A MICELLE-TYPE STRUCTURE, AND THE OBSERVED DENSITY FOR THESE LIGANDS IS COMPLETELY CONSISTENT WITH THE PACKING REQUIREMENTS OF THE NEIGHBORING LDA MOLECULES.

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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: 3.12 Å3/Da / Density % sol: 60.56 %
Crystal growTemperature: 300 K / Method: vapor diffusion / pH: 6.5
Details: 1.6 M trisodium citrate, pH 6.5, VAPOR DIFFUSION, temperature 300K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONAPS 19-ID11.009
ROTATING ANODERIGAKU FR-E+ SUPERBRIGHT22.292
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDJul 25, 2009
RIGAKU RAXIS IV++2IMAGE PLATEOct 10, 2009
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SAGITALLY FOCUSED Si(111)SINGLE WAVELENGTHMx-ray1
2VariMax CrSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.0091
22.2921
ReflectionResolution: 1.9→34.5 Å / Num. all: 10065 / Num. obs: 9934 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.1 % / Biso Wilson estimate: 31.3 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 44.9
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.443 / Mean I/σ(I) obs: 3.2 / % possible all: 98.1

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0102refinement
PDB_EXTRACT3.1data extraction
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
SHELXSphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→10 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.913 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 8.515 / SU ML: 0.118 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.28 478 4.8 %RANDOM
Rwork0.23 ---
obs0.232 9889 99.3 %-
all-9889 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.21 Å2
Baniso -1Baniso -2Baniso -3
1-1.05 Å20.52 Å20 Å2
2--1.05 Å20 Å2
3----1.57 Å2
Refinement stepCycle: LAST / Resolution: 1.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms606 0 320 65 991
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.021917
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.92.3011179
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.576579
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.43427.72722
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.67415116
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.914151
X-RAY DIFFRACTIONr_chiral_restr0.1120.2101
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021439
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1961.5401
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.192653
X-RAY DIFFRACTIONr_scbond_it2.8253516
X-RAY DIFFRACTIONr_scangle_it4.554.5526
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 32 -
Rwork0.208 630 -
obs--98.66 %
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)
11.1858-0.2517-0.19083.46120.87371.3810.02390.05140.05210.00160.1416-0.40360.0070.0121-0.16560.0322-0.00920.00420.0918-0.0480.075129.558-4.286-16.28
20.52040.34991.31221.11371.05823.35820.0852-0.0733-0.02980.0086-0.0142-0.00460.1719-0.1482-0.0710.0279-0.0311-0.0010.1063-0.03280.051120.22713.50.31
30.89330.49570.88331.25051.20012.4564-0.1062-0.2654-0.023-0.0576-0.11620.30450.3517-0.10020.22240.24010.04660.02610.13460.00830.109922.584-0.148-4.168
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 17
2X-RAY DIFFRACTION1A68 - 80
3X-RAY DIFFRACTION2A18 - 67
4X-RAY DIFFRACTION3A101
5X-RAY DIFFRACTION3A102
6X-RAY DIFFRACTION3A103
7X-RAY DIFFRACTION3A104
8X-RAY DIFFRACTION3A105
9X-RAY DIFFRACTION3A106
10X-RAY DIFFRACTION3A107
11X-RAY DIFFRACTION3A108
12X-RAY DIFFRACTION3A109
13X-RAY DIFFRACTION3A110
14X-RAY DIFFRACTION3A111
15X-RAY DIFFRACTION3A112
16X-RAY DIFFRACTION3A113
17X-RAY DIFFRACTION3A114
18X-RAY DIFFRACTION3A115
19X-RAY DIFFRACTION3A116
20X-RAY DIFFRACTION3A117
21X-RAY DIFFRACTION3A118
22X-RAY DIFFRACTION3A119
23X-RAY DIFFRACTION3A120

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