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- PDB-3s63: Saposin-like protein Na-SLP-1 -

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Basic information

Entry
Database: PDB / ID: 3s63
TitleSaposin-like protein Na-SLP-1
ComponentsSaposin-like protein
KeywordsLIPID BINDING PROTEIN / saposin / lipid-binding
Function / homologySaposin-like / NK-Lysin / Saposin B type domain / Saposin-like / Saposin B type domain profile. / Orthogonal Bundle / Mainly Alpha / Saposin-like protein
Function and homology information
Biological speciesNecator americanus (New World hookworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.7 Å
AuthorsWillis, C. / Wang, C.K. / Osman, A. / Simon, A. / Mulvenna, J. / Pickering, D. / Riboldi-Tunicliffe, A. / Jones, M.K. / Loukas, A. / Hofmann, A.
CitationJournal: Plos One / Year: 2011
Title: Insights into the membrane interactions of the saposin-like proteins Na-SLP-1 and Ac-SLP-1 from human and dog hookworm.
Authors: Willis, C. / Wang, C.K. / Osman, A. / Simon, A. / Pickering, D. / Mulvenna, J. / Riboldi-Tunicliffe, A. / Jones, M.K. / Loukas, A. / Hofmann, A.
History
DepositionMay 24, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 18, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Saposin-like protein
B: Saposin-like protein


Theoretical massNumber of molelcules
Total (without water)27,1312
Polymers27,1312
Non-polymers00
Water70339
1
A: Saposin-like protein


Theoretical massNumber of molelcules
Total (without water)13,5661
Polymers13,5661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Saposin-like protein


Theoretical massNumber of molelcules
Total (without water)13,5661
Polymers13,5661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)85.433, 85.433, 113.452
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Saposin-like protein / Na-SLP-1


Mass: 13565.567 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Necator americanus (New World hookworm)
Production host: Pichia pastoris (fungus) / References: UniProt: H2L2M0*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsA SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST.

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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: 2.2 Å3/Da / Density % sol: 44.16 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2M NaCl, 20% PEG 6000, 0.1M HEPES, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.94723 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 7, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.94723 Å / Relative weight: 1
ReflectionResolution: 2.7→25 Å / Num. obs: 7191 / % possible obs: 99.9 % / Redundancy: 41.7 % / Biso Wilson estimate: 56 Å2 / Rsym value: 0.101 / Net I/σ(I): 7.4
Reflection shellHighest resolution: 2.7 Å / Redundancy: 43 % / Num. unique all: 1021 / Rsym value: 0.515 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHARPphasing
PHENIX(phenix.refine: 1.6.1_357)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SIRAS / Resolution: 2.7→24.662 Å / SU ML: 0.36 / σ(F): 1.49 / Phase error: 24.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2449 595 4.68 %RANDOM
Rwork0.1845 ---
obs0.1874 7191 99.97 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.004 Å2 / ksol: 0.362 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--10.6589 Å2-0 Å20 Å2
2---10.6589 Å2-0 Å2
3---21.3178 Å2
Refinement stepCycle: LAST / Resolution: 2.7→24.662 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1400 0 0 39 1439
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081433
X-RAY DIFFRACTIONf_angle_d1.1471919
X-RAY DIFFRACTIONf_dihedral_angle_d17.584552
X-RAY DIFFRACTIONf_chiral_restr0.078215
X-RAY DIFFRACTIONf_plane_restr0.005248
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.7001-2.97140.27111680.21133005
2.9714-3.40040.31781530.19073027
3.4004-4.28050.20151320.16763048
4.2805-24.66340.21641420.18083040

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