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- PDB-2ygn: WIF domain of human Wnt inhibitory factor 1 in complex with 1,2- ... -

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Basic information

Entry
Database: PDB / ID: 2ygn
TitleWIF domain of human Wnt inhibitory factor 1 in complex with 1,2- dipalmitoylphosphatidylcholine
ComponentsWNT INHIBITORY FACTOR 1
KeywordsSIGNALING PROTEIN / WNT SIGNALING PATHWAY / WNT ANTAGONIST / MORPHOGEN / CANCER / GLYCOSAMINOGLYCAN
Function / homology
Function and homology information


Negative regulation of TCF-dependent signaling by WNT ligand antagonists / Wnt-protein binding / negative regulation of Wnt signaling pathway / positive regulation of fat cell differentiation / TCF dependent signaling in response to WNT / Wnt signaling pathway / signaling receptor binding / cell surface / signal transduction / extracellular region
Similarity search - Function
Wnt inhibitory factor (WIF)-1 / : / Wnt, WIF domain / WIF domain / WIF domain superfamily / WIF domain / WIF domain profile. / Wnt-inhibitory factor-1 like domain / Delta-like/Jagged, EGF-like domain / EGF-like, conserved site ...Wnt inhibitory factor (WIF)-1 / : / Wnt, WIF domain / WIF domain / WIF domain superfamily / WIF domain / WIF domain profile. / Wnt-inhibitory factor-1 like domain / Delta-like/Jagged, EGF-like domain / EGF-like, conserved site / Human growth factor-like EGF / Epidermal growth factor-like domain. / EGF-like domain profile. / EGF-like domain signature 1. / EGF-like domain signature 2. / EGF-like domain / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / 1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE / Wnt inhibitory factor 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsMalinauskas, T. / Aricescu, A.R. / Lu, W. / Siebold, C. / Jones, E.Y.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2011
Title: Modular Mechanism of Wnt Signaling Inhibition by Wnt Inhibitory Factor 1
Authors: Malinauskas, T. / Aricescu, A.R. / Lu, W. / Siebold, C. / Jones, E.Y.
History
DepositionApr 19, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 20, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2011Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / 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_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: WNT INHIBITORY FACTOR 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6244
Polymers17,6091
Non-polymers1,0143
Water1,49583
1
A: WNT INHIBITORY FACTOR 1
hetero molecules

A: WNT INHIBITORY FACTOR 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2478
Polymers35,2182
Non-polymers2,0296
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_445-x-1/2,-y-1/2,z1
Buried area5110 Å2
ΔGint-44.2 kcal/mol
Surface area15650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.912, 134.138, 60.378
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222

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Components

#1: Protein WNT INHIBITORY FACTOR 1 / WIF-1


Mass: 17609.219 Da / Num. of mol.: 1 / Fragment: WIF DOMAIN, RESIDUES 35-178
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human)
Cell line (production host): N-ACETYLGLUCOSAMINYLTRANSFERASE I-NEGATIVE HEK 293S GNTI(-)CELLS
Production host: HOMO SAPIENS (human) / References: UniProt: Q9Y5W5
#2: Chemical ChemComp-PCF / 1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE


Mass: 734.039 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H80NO8P
#3: 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
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsISOFORM Q166K. CRYSTALLISATION CONSTRUCT CONTAINS N- TERMINAL ETG AND C-TERMINAL GTKHHHHHH AMINO ...ISOFORM Q166K. CRYSTALLISATION CONSTRUCT CONTAINS N- TERMINAL ETG AND C-TERMINAL GTKHHHHHH AMINO ACID RESIDUES DERIVED FROM THE EXPRESSION VECTOR.

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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: 2.87 Å3/Da / Density % sol: 57 % / Description: NONE
Crystal growpH: 6.5
Details: PEG 8000 30 % W/V, 200 MM SODIUM ACETATE, 100 MM SODIUM CACODYLATE PH 6.5 .

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.978
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.85→30 Å / Num. obs: 17655 / % possible obs: 98.8 % / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 16.3
Reflection shellResolution: 1.85→1.93 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 1.4 / % possible all: 91.3

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.7_650)refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2D3J

2d3j


Resolution: 1.85→27.529 Å / SU ML: 0.22 / σ(F): 0 / Phase error: 26.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2239 828 5.1 %
Rwork0.2039 --
obs0.205 16407 92.48 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.123 Å2 / ksol: 0.353 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-18.7533 Å20 Å20 Å2
2---13.9848 Å20 Å2
3----4.7685 Å2
Refinement stepCycle: LAST / Resolution: 1.85→27.529 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1151 0 68 83 1302
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0151245
X-RAY DIFFRACTIONf_angle_d2.2241673
X-RAY DIFFRACTIONf_dihedral_angle_d21.154483
X-RAY DIFFRACTIONf_chiral_restr0.141186
X-RAY DIFFRACTIONf_plane_restr0.009202
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8501-1.9660.40371260.33662107X-RAY DIFFRACTION77
1.966-2.11770.31911340.24482466X-RAY DIFFRACTION89
2.1177-2.33070.25651500.21792572X-RAY DIFFRACTION93
2.3307-2.66780.24611360.20772701X-RAY DIFFRACTION97
2.6678-3.36020.23381400.18942795X-RAY DIFFRACTION99
3.3602-27.53180.17131420.18692938X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -3.1903 Å / Origin y: -17.5302 Å / Origin z: 15.0452 Å
111213212223313233
T0.2686 Å2-0.02 Å2-0.0189 Å2-0.252 Å2-0.0023 Å2--0.2591 Å2
L1.5263 °20.0931 °20.1551 °2-1.0058 °2-0.4158 °2--1.5368 °2
S-0.0456 Å °-0.0482 Å °0.1734 Å °0.0093 Å °0.015 Å °-0.0629 Å °-0.315 Å °0.0817 Å °0 Å °
Refinement TLS groupSelection details: ALL

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