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Yorodumi- PDB-2ygp: WIF domain-EGF-like domain 1 Met77Trp of human Wnt inhibitory fac... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ygp | ||||||
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Title | WIF domain-EGF-like domain 1 Met77Trp of human Wnt inhibitory factor 1 in complex with 1,2-dipalmitoylphosphatidylcholine | ||||||
Components | WNT INHIBITORY FACTOR 1 | ||||||
Keywords | SIGNALING 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 | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.222 Å | ||||||
Authors | Malinauskas, T. / Aricescu, A.R. / Lu, W. / Siebold, C. / Jones, E.Y. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ygp.cif.gz | 90.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ygp.ent.gz | 72.1 KB | Display | PDB format |
PDBx/mmJSON format | 2ygp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yg/2ygp ftp://data.pdbj.org/pub/pdb/validation_reports/yg/2ygp | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | 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 |
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#3: Sugar | ChemComp-NAG / |
-Non-polymers , 4 types, 114 molecules
#2: Chemical | ChemComp-PCF / |
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#4: Chemical | ChemComp-CA / |
#5: Chemical | ChemComp-SPD / |
#6: Water | ChemComp-HOH / |
-Details
Compound details | ENGINEEREDSequence details | ISOFORM 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 CRYSTALLIS | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 50 % / Description: NONE |
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Crystal grow | pH: 7 Details: 1.1 M DIAMMONIUM TARTRATE, PH 7.0, 20 MM SPERMIDINE, 0.5 MM CACL2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.978 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 2.22→2.28 Å / Redundancy: 6 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2.3 / % possible all: 92 |
-Processing
Software |
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Refinement | Method 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
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Solvent computation | Shrinkage 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 parameters | Biso mean: 51.04 Å2
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Refinement step | Cycle: LAST / Resolution: 2.222→29.316 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -6.8842 Å / Origin y: -13.275 Å / Origin z: 14.904 Å
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Refinement TLS group | Selection details: ALL |