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- PDB-6gbi: Wnt signalling -

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Basic information

Entry
Database: PDB / ID: 6gbi
TitleWnt signalling
ComponentsLy6/PLAUR domain-containing protein 6
KeywordsSTRUCTURAL PROTEIN / Wnt
Function / homology
Function and homology information


acetylcholine receptor inhibitor activity / side of membrane / positive regulation of canonical Wnt signaling pathway / perikaryon / membrane raft / synapse / dendrite / extracellular region / plasma membrane / cytoplasm
Similarity search - Function
Ly6/PLAUR domain-containing protein 6-like / Ly6/PLAUR domain-containing protein 6, Lypd6 / Snake toxin-like superfamily
Similarity search - Domain/homology
Ly6/PLAUR domain-containing protein 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / molecular replacement / Resolution: 1.25 Å
AuthorsZhao, Y. / Jones, E.Y.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MR/M000141/1 United Kingdom
CitationJournal: FEBS Lett. / Year: 2018
Title: Structure of the Wnt signaling enhancer LYPD6 and its interactions with the Wnt coreceptor LRP6.
Authors: Zhao, Y. / Ren, J. / Lu, W. / Harlos, K. / Jones, E.Y.
History
DepositionApr 14, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 15, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ly6/PLAUR domain-containing protein 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3086
Polymers11,7101
Non-polymers5985
Water1,67593
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area980 Å2
ΔGint-24 kcal/mol
Surface area6980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.980, 61.980, 68.550
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-377-

HOH

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Components

#1: Protein Ly6/PLAUR domain-containing protein 6


Mass: 11710.120 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LYPD6, UNQ3023/PRO9821
Production host: Mammalian expression vector pCI-NEO-FLAG-SMNdelta3,4,5,6,7 (others)
References: UniProt: Q86Y78
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.81 Å3/Da / Density % sol: 56.24 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 Tris-HCl 2M Ammonium Sulphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Feb 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.25→50 Å / Num. obs: 37608 / % possible obs: 100 % / Redundancy: 12.3 % / Net I/σ(I): 31.2
Reflection shellResolution: 1.25→1.28 Å

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Phasing

Phasing
Method
SAD
molecular replacement

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Processing

Software
NameVersionClassification
DENZOdata reduction
xia2data scaling
PHASERphasing
SHARPphasing
RESOLVEphasing
REFMAC5.8.0189refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: SAD / Resolution: 1.25→45.97 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.969 / SU B: 1.007 / SU ML: 0.02 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.038 / ESU R Free: 0.034
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1646 1877 5 %RANDOM
Rwork0.1621 ---
obs0.1623 35666 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 61.55 Å2 / Biso mean: 21.854 Å2 / Biso min: 11.76 Å2
Baniso -1Baniso -2Baniso -3
1--0.59 Å20 Å20 Å2
2---0.59 Å20 Å2
3---1.17 Å2
Refinement stepCycle: final / Resolution: 1.25→45.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms809 0 36 93 938
Biso mean--34.38 30.54 -
Num. residues----104
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.019871
X-RAY DIFFRACTIONr_bond_other_d0.0010.02736
X-RAY DIFFRACTIONr_angle_refined_deg1.1641.9881186
X-RAY DIFFRACTIONr_angle_other_deg1.04731727
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5395105
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.31724.3941
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.4915138
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.278156
X-RAY DIFFRACTIONr_chiral_restr0.0670.2133
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021950
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02167
X-RAY DIFFRACTIONr_rigid_bond_restr0.80231607
X-RAY DIFFRACTIONr_sphericity_free16.274556
X-RAY DIFFRACTIONr_sphericity_bonded8.61451624
LS refinement shellResolution: 1.25→1.282 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2 134 -
Rwork0.174 2576 -
all-2710 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 24.1599 Å / Origin y: 52.6364 Å / Origin z: 24.9349 Å
111213212223313233
T0.0019 Å20.0002 Å20.0013 Å2-0.0009 Å2-0.0002 Å2--0.002 Å2
L0.2959 °20.0517 °20.1918 °2-0.1806 °20.01 °2--0.1369 °2
S0.0032 Å °0.0024 Å °0.006 Å °0.0006 Å °-0.0039 Å °0.0008 Å °0.0012 Å °0.0042 Å °0.0007 Å °

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