+Open data
-Basic information
Entry | Database: PDB / ID: 5fwv | ||||||
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Title | Wnt modulator Kremen crystal form III at 3.2A | ||||||
Components | KREMEN PROTEIN 1 | ||||||
Keywords | SIGNALING PROTEIN / WNT / CELL SURFACE / SIGNALLING / MEMBRANE PROTEIN | ||||||
Function / homology | Function and homology information Signaling by LRP5 mutants / Negative regulation of TCF-dependent signaling by WNT ligand antagonists / negative regulation of axon regeneration / cell communication / negative regulation of ossification / regulation of canonical Wnt signaling pathway / limb development / TCF dependent signaling in response to WNT / negative regulation of canonical Wnt signaling pathway / Wnt signaling pathway ...Signaling by LRP5 mutants / Negative regulation of TCF-dependent signaling by WNT ligand antagonists / negative regulation of axon regeneration / cell communication / negative regulation of ossification / regulation of canonical Wnt signaling pathway / limb development / TCF dependent signaling in response to WNT / negative regulation of canonical Wnt signaling pathway / Wnt signaling pathway / neuronal cell body / apoptotic process / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 3.2 Å | ||||||
Authors | Zebisch, M. / Jackson, V.A. / Jones, E.Y. | ||||||
Citation | Journal: Structure / Year: 2016 Title: Structure of the Dual-Mode Wnt Regulator Kremen1 and Insight Into Ternary Complex Formation with Lrp6 and Dickkopf Authors: Zebisch, M. / Jackson, V.A. / Zhao, Y. / 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 | 5fwv.cif.gz | 130.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fwv.ent.gz | 104.3 KB | Display | PDB format |
PDBx/mmJSON format | 5fwv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fw/5fwv ftp://data.pdbj.org/pub/pdb/validation_reports/fw/5fwv | 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 44551.777 Da / Num. of mol.: 1 / Fragment: ECD, RESIDUES 29-373 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PHLSEC / Cell line (production host): HEK293 / Production host: HOMO SAPIENS (human) / References: UniProt: Q96MU8 | ||||
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#2: Chemical | ChemComp-CL / #3: Sugar | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.3 Å3/Da / Density % sol: 62.6 % / Description: NONE |
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Crystal grow | pH: 7.5 / Details: 0.1 M HEPES/MOPS 7.5 30 % P550MME_P20K DRIED OUT |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 |
Detector | Type: DECTRIS PILATUS / Detector: PIXEL / Date: Sep 15, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→67.8 Å / Num. obs: 8171 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 22.7 % / Biso Wilson estimate: 76.6 Å2 / Rmerge(I) obs: 0.3 / Net I/σ(I): 13.1 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER Starting model: NONE Resolution: 3.2→64.19 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.864 / SU B: 53.731 / SU ML: 0.401 / Cross valid method: THROUGHOUT / ESU R Free: 0.476 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 75.628 Å2
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Refinement step | Cycle: LAST / Resolution: 3.2→64.19 Å
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Refine LS restraints |
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