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- PDB-2ygp: WIF domain-EGF-like domain 1 Met77Trp of human Wnt inhibitory fac... -

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Basic information

Entry
Database: PDB / ID: 2ygp
TitleWIF domain-EGF-like domain 1 Met77Trp 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 / SPERMIDINE / Wnt inhibitory factor 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.222 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 / 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

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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)22,2725
Polymers21,1311
Non-polymers1,1414
Water2,000111
1
A: WNT INHIBITORY FACTOR 1
hetero molecules

A: WNT INHIBITORY FACTOR 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,54310
Polymers42,2622
Non-polymers2,2818
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area6220 Å2
ΔGint-52.4 kcal/mol
Surface area19210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.760, 134.241, 60.193
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222

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Components

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Protein / Sugars , 2 types, 2 molecules A

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


Mass: 21131.082 Da / Num. of mol.: 1 / Fragment: WIF DOMAIN-EGF-LIKE DOMAIN 1, RESIDUES 35-210 / Mutation: YES
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
#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

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Non-polymers , 4 types, 114 molecules

#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
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-SPD / SPERMIDINE / N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE / PA(34) / Spermidine


Mass: 145.246 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H19N3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 111 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, MET 77 TO TRP
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, CONTAINS MET77TRP MUTATION.

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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: 2.29 Å3/Da / Density % sol: 50 % / Description: NONE
Crystal growpH: 7
Details: 1.1 M DIAMMONIUM TARTRATE, PH 7.0, 20 MM SPERMIDINE, 0.5 MM CACL2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.978
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.22→29.32 Å / Num. obs: 10433 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Biso Wilson estimate: 35.19 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 12.7
Reflection shellResolution: 2.22→2.28 Å / Redundancy: 6 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2.3 / % possible all: 92

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.222→29.316 Å / SU ML: 0.33 / σ(F): 0 / Phase error: 21.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2289 502 4.8 %
Rwork0.1855 --
obs0.1875 10431 99.33 %
Solvent computationShrinkage radii: 0.61 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 55.777 Å2 / ksol: 0.365 e/Å3
Displacement parametersBiso mean: 51.04 Å2
Baniso -1Baniso -2Baniso -3
1-8.8036 Å20 Å20 Å2
2---7.9788 Å20 Å2
3----0.8248 Å2
Refinement stepCycle: LAST / Resolution: 2.222→29.316 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1406 0 75 111 1592
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0151520
X-RAY DIFFRACTIONf_angle_d2.2172037
X-RAY DIFFRACTIONf_dihedral_angle_d19.537587
X-RAY DIFFRACTIONf_chiral_restr0.149214
X-RAY DIFFRACTIONf_plane_restr0.009255
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.222-2.44550.29461270.24992363X-RAY DIFFRACTION97
2.4455-2.79910.29491340.20712455X-RAY DIFFRACTION100
2.7991-3.52560.19661200.16872501X-RAY DIFFRACTION100
3.5256-29.31890.20931210.17472610X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -6.8842 Å / Origin y: -13.275 Å / Origin z: 14.904 Å
111213212223313233
T0.1811 Å2-0.0042 Å2-0.0173 Å2-0.2028 Å20.002 Å2--0.1779 Å2
L0.7809 °20.3848 °20.1523 °2-0.4618 °2-0.2585 °2--0.7642 °2
S-0.0362 Å °-0.0262 Å °0.1149 Å °0.006 Å °0.0385 Å °0.093 Å °-0.1032 Å °-0.0672 Å °-0.0008 Å °
Refinement TLS groupSelection details: ALL

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