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- PDB-4v2o: Structure of saposin B in complex with chloroquine -

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Basic information

Entry
Database: PDB / ID: 4v2o
TitleStructure of saposin B in complex with chloroquine
ComponentsSAPOSIN-B
KeywordsHYDROLASE ACTIVATOR / PROTEIN-LIGAND COMPLEX
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 / 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
Chem-CLQ / Prosaposin
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 Å
AuthorsZubieta, C. / Lai, X. / Doyle, R.P.
CitationJournal: Chemmedchem / Year: 2016
Title: The Lysosomal Protein Saposin B Binds Chloroquine.
Authors: Huta, B.P. / Mehlenbacher, M.R. / Nie, Y. / Lai, X. / Zubieta, C. / Bou-Abdallah, F. / Doyle, R.P.
History
DepositionOct 13, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 9, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 2, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
C: SAPOSIN-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9325
Polymers27,2923
Non-polymers6402
Water2,666148
1
A: SAPOSIN-B
C: SAPOSIN-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5153
Polymers18,1952
Non-polymers3201
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2360 Å2
ΔGint-22.7 kcal/mol
Surface area9960 Å2
MethodPISA
2
B: SAPOSIN-B
hetero molecules

B: SAPOSIN-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8354
Polymers18,1952
Non-polymers6402
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_677x-y+1,-y+2,-z+7/31
Buried area3390 Å2
ΔGint-25.4 kcal/mol
Surface area9750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.299, 75.299, 94.716
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11B-2016-

HOH

21B-2020-

HOH

31B-2042-

HOH

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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 / SAPOSIN B


Mass: 9097.452 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): SHUFFLE EXPRESS / References: UniProt: P07602
#2: Chemical ChemComp-CLQ / N4-(7-CHLORO-QUINOLIN-4-YL)-N1,N1-DIETHYL-PENTANE-1,4-DIAMINE / CHLOROQUINE


Mass: 319.872 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H26ClN3 / Comment: medication*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / 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: 2.77 Å3/Da / Density % sol: 50 % / Description: NONE
Crystal growpH: 6.5 / Details: 0.1M MES, PH 6.0, 30% PEG6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.99187
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 30, 2014
RadiationMonochromator: SI(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99187 Å / Relative weight: 1
ReflectionResolution: 2.13→38 Å / Num. obs: 17890 / % possible obs: 98.9 % / Observed criterion σ(I): 1.6 / Redundancy: 6.9 % / Biso Wilson estimate: 43.94 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 14.4
Reflection shellResolution: 2.13→2.2 Å / Redundancy: 6.9 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 1.6 / % possible all: 92.5

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1N69

1n69


Resolution: 2.13→15 Å / Cor.coef. Fo:Fc: 0.9187 / Cor.coef. Fo:Fc free: 0.8936 / SU R Cruickshank DPI: 0.224 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.241 / SU Rfree Blow DPI: 0.188 / SU Rfree Cruickshank DPI: 0.182
RfactorNum. reflection% reflectionSelection details
Rfree0.2538 908 5.13 %RANDOM
Rwork0.229 ---
obs0.2303 17711 99.59 %-
Displacement parametersBiso mean: 65.52 Å2
Baniso -1Baniso -2Baniso -3
1--7.2465 Å20 Å20 Å2
2---7.2465 Å20 Å2
3---14.4929 Å2
Refine analyzeLuzzati coordinate error obs: 0.369 Å
Refinement stepCycle: LAST / Resolution: 2.13→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1806 0 44 148 1998
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0091926HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.082602HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d696SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes59HARMONIC2
X-RAY DIFFRACTIONt_gen_planes269HARMONIC5
X-RAY DIFFRACTIONt_it1926HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.13
X-RAY DIFFRACTIONt_other_torsion16.85
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion264SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2362SEMIHARMONIC4
LS refinement shellResolution: 2.13→2.26 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.2313 148 5.29 %
Rwork0.2279 2648 -
all0.228 2796 -
obs--99.59 %
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)
12.6038-0.0929-0.30433.2607-1.00594.8209-0.0675-0.42870.19750.08970.14950.0135-0.36-0.3492-0.0820.10290.0973-0.0220.0876-0.0655-0.01284.81684.3038109.524
23.96760.81720.8642.80051.27954.74930.0720.42020.0863-0.27370.0916-0.3922-0.40711.1666-0.16370.0417-0.04130.08690.39320.01930.01934.343569.9897106.363
32.5777-0.7454-1.09052.9414-1.74186.04110.01750.48350.2014-0.06380.39240.2729-0.2643-1.1597-0.40990.15570.0363-0.07180.2420.11350.0588-4.326682.6001100.582
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|1 - A|78 }
2X-RAY DIFFRACTION2{ B|-2 - B|78 }
3X-RAY DIFFRACTION3{ C|-2 - C|78 }

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