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- PDB-2ygo: WIF domain-EGF-like domain 1 of human Wnt inhibitory factor 1 in ... -

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Basic information

Entry
Database: PDB / ID: 2ygo
TitleWIF domain-EGF-like domain 1 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


nodal binding / nodal signaling pathway / Negative regulation of TCF-dependent signaling by WNT ligand antagonists / activin receptor binding / Wnt-protein binding / determination of left/right symmetry / anterior/posterior pattern specification / negative regulation of Wnt signaling pathway / blood vessel development / positive regulation of fat cell differentiation ...nodal binding / nodal signaling pathway / Negative regulation of TCF-dependent signaling by WNT ligand antagonists / activin receptor binding / Wnt-protein binding / determination of left/right symmetry / anterior/posterior pattern specification / negative regulation of Wnt signaling pathway / blood vessel development / positive regulation of fat cell differentiation / TCF dependent signaling in response to WNT / Wnt signaling pathway / heart development / cell surface / signal transduction / extracellular region
Similarity search - Function
Wnt, WIF domain / Wnt inhibitory factor (WIF)-1 / 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 ...Wnt, WIF domain / Wnt inhibitory factor (WIF)-1 / 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 / Laminin / Laminin / Epidermal growth factor-like domain. / EGF-like domain profile. / EGF-like domain signature 2. / EGF-like domain signature 1. / EGF-like domain / Ribbon / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
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 13, 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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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)22,0544
Polymers21,0761
Non-polymers9783
Water2,720151
1
A: WNT INHIBITORY FACTOR 1
hetero molecules

A: WNT INHIBITORY FACTOR 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1098
Polymers42,1522
Non-polymers1,9566
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area6200 Å2
ΔGint-59 kcal/mol
Surface area19190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.996, 134.260, 60.403
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: 21076.068 Da / Num. of mol.: 1 / Fragment: WIF DOMAIN-EGF-LIKE DOMAIN 1, RESIDUES 35-210
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 / Dipalmitoylphosphatidylcholine


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-Acetylglucosamine


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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 151 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsISOFORM Q166K. THE N-TERMINAL THREE AMINO ACID RESIDUES (ETG) AND C-TERMINAL NINE AMINO ACID ...ISOFORM Q166K. THE N-TERMINAL THREE AMINO ACID RESIDUES (ETG) AND C-TERMINAL NINE AMINO ACID RESIDUES (GTKHHHHHH) OF THE CRYSTALLISATION CONSTRUCT ARE DERIVED FROM THE PHLSEC 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: 2.45 Å3/Da / Density % sol: 50 % / Description: NONE
Crystal growpH: 7
Details: 1.3 M DIAMMONIUM TARTRATE, 100 MM BIS-TRIS PROPANE PH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873
DetectorType: MARRESEARCH / Detector: CCD
RadiationMonochromator: HORIZONTALLY SIDE DIFFRACTING SILICON 111 CRYSTAL
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 1.85→40 Å / Num. obs: 18293 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Biso Wilson estimate: 17.56 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 15.5
Reflection shellResolution: 1.85→1.99 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.94 / Mean I/σ(I) obs: 1.9 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→37.422 Å / SU ML: 0.24 / σ(F): 0 / Phase error: 20.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2168 886 5.2 %
Rwork0.1839 --
obs0.1856 17107 94.26 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.411 Å2 / ksol: 0.346 e/Å3
Displacement parametersBiso mean: 36.27 Å2
Baniso -1Baniso -2Baniso -3
1-5.9344 Å20 Å20 Å2
2---4.8759 Å20 Å2
3----1.0585 Å2
Refinement stepCycle: LAST / Resolution: 1.85→37.422 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1400 0 65 151 1616
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0151508
X-RAY DIFFRACTIONf_angle_d2.0692025
X-RAY DIFFRACTIONf_dihedral_angle_d18.794584
X-RAY DIFFRACTIONf_chiral_restr0.152216
X-RAY DIFFRACTIONf_plane_restr0.008255
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.96590.27871470.23642360X-RAY DIFFRACTION85
1.9659-2.11770.26381340.19312576X-RAY DIFFRACTION91
2.1177-2.33080.2321600.18662681X-RAY DIFFRACTION95
2.3308-2.6680.22691490.18532736X-RAY DIFFRACTION96
2.668-3.3610.21681510.17262856X-RAY DIFFRACTION99
3.361-37.42940.18311450.17723012X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -7.104 Å / Origin y: -13.2309 Å / Origin z: 14.838 Å
111213212223313233
T0.0225 Å2-0.0117 Å2-0.016 Å2-0.0237 Å20.002 Å2--0.0358 Å2
L0.9297 °20.4263 °20.0996 °2-0.5518 °2-0.009 °2--1.0348 °2
S-0.0336 Å °-0.0007 Å °0.1715 Å °-0.0312 Å °0.0257 Å °0.0797 Å °-0.0979 Å °-0.0863 Å °0.0012 Å °
Refinement TLS groupSelection details: ALL

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