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- PDB-6slr: Structure of saposin B in complex with atovaquone -

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Basic information

Entry
Database: PDB / ID: 6slr
TitleStructure of saposin B in complex with atovaquone
ComponentsProsaposin
KeywordsLIPID BINDING PROTEIN / glycoprotein / lysosome / protein-ligand complex / atovaquone
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
Chem-AOQ / Prosaposin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 Å
AuthorsZubieta, C. / Milliken, B. / Doyle, R.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyATIP-Avenir France
CitationJournal: To Be Published
Title: Structure of saposin B in complex with atovaquone
Authors: Zubieta, C. / Milliken, B. / Doyle, R.
History
DepositionAug 20, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 9, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Prosaposin
B: Prosaposin
C: Prosaposin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9158
Polymers26,9053
Non-polymers1,0105
Water1,04558
1
A: Prosaposin
C: Prosaposin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3964
Polymers17,9372
Non-polymers4592
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Prosaposin
hetero molecules

B: Prosaposin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0398
Polymers17,9372
Non-polymers1,1026
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_675x-y+1,-y+2,-z+1/31
Unit cell
Length a, b, c (Å)75.707, 75.707, 95.475
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11B-203-

AOQ

21B-203-

AOQ

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERCYSCYSAA0 - 773 - 80
21SERSERCYSCYSBB0 - 773 - 80
12SERSERCYSCYSAA0 - 773 - 80
22SERSERCYSCYSCC0 - 773 - 80
13GLYGLYASPASPBB-2 - 781 - 81
23GLYGLYASPASPCC-2 - 781 - 81

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Prosaposin / Proactivator polypeptide


Mass: 8968.339 Da / Num. of mol.: 3
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-AOQ / 2-[trans-4-(4-chlorophenyl)cyclohexyl]-3-hydroxynaphthalene-1,4-dione / Atovaquone


Mass: 366.837 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H19ClO3 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, Antimicrobial*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.96 Å3/Da / Density % sol: 58.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M MES, 30% PEG6000 / PH range: 5-6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Aug 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 1.91→38.62 Å / Num. obs: 14331 / % possible obs: 91.8 % / Redundancy: 5.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.025 / Rrim(I) all: 0.063 / Net I/σ(I): 15.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.927-2.182.40.4167180.8250.3120.52371.1
6.455-38.65.60.0287170.9990.0130.03198.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
Aimlessdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4V2O

4v2o


Resolution: 2.38→38.62 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.926 / SU B: 20.247 / SU ML: 0.221 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.38 / ESU R Free: 0.271 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2777 715 5.5 %RANDOM
Rwork0.2326 ---
obs0.2349 12391 99.46 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso max: 138.3 Å2 / Biso mean: 76.973 Å2 / Biso min: 40.07 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20.04 Å20 Å2
2--0.08 Å2-0 Å2
3----0.25 Å2
Refinement stepCycle: final / Resolution: 2.38→38.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1835 0 96 58 1989
Biso mean--88.8 71.31 -
Num. residues----240
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0131974
X-RAY DIFFRACTIONr_bond_other_d0.0010.0181771
X-RAY DIFFRACTIONr_angle_refined_deg1.3431.72669
X-RAY DIFFRACTIONr_angle_other_deg1.271.6194143
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9645240
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.32225.33390
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.33915349
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.571156
X-RAY DIFFRACTIONr_chiral_restr0.0660.2267
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022163
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02353
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A22290.1
12B22290.1
21A22170.1
22C22170.1
31B23020.11
32C23020.11
LS refinement shellResolution: 2.38→2.44 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.308 50 -
Rwork0.322 898 -
obs--97.53 %
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)
12.67110.2762-0.05412.8979-0.92424.60.01170.491-0.4316-0.0980.07960.13610.4768-0.3809-0.09130.1432-0.0774-0.00080.1697-0.07290.084342.456-19.12816.972
25.268-0.0379-2.19953.16541.62746.1498-0.0065-0.5543-0.29640.37980.1368-0.56240.49271.339-0.13030.1180.033-0.08360.39740.03640.124334.59760.89920.023
33.5512-0.00240.3652.8574-1.34915.7790.0616-0.4422-0.39370.13070.26050.39860.4873-0.921-0.32210.2626-0.01770.07590.22940.11680.129733.442-17.41525.88
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 78
2X-RAY DIFFRACTION2B-2 - 78
3X-RAY DIFFRACTION3C-2 - 78

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