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- PDB-1ijx: CRYSTAL STRUCTURE OF THE CYSTEINE-RICH DOMAIN OF SECRETED FRIZZLE... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ijx | ||||||
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Title | CRYSTAL STRUCTURE OF THE CYSTEINE-RICH DOMAIN OF SECRETED FRIZZLED-RELATED PROTEIN 3 (SFRP-3;FZB) | ||||||
![]() | SECRETED FRIZZLED-RELATED SEQUENCE PROTEIN 3 | ||||||
![]() | SIGNALING PROTEIN / WNT RECEPTOR / FRIZZLED PROTEIN STRUCTURE / CYSTEINE-RICH | ||||||
Function / homology | ![]() negative regulation of hepatocyte differentiation / negative regulation of cell development / convergent extension involved in organogenesis / cochlea morphogenesis / negative regulation of cartilage development / somite development / Wnt-protein binding / neural crest cell differentiation / inner ear morphogenesis / negative regulation of Wnt signaling pathway ...negative regulation of hepatocyte differentiation / negative regulation of cell development / convergent extension involved in organogenesis / cochlea morphogenesis / negative regulation of cartilage development / somite development / Wnt-protein binding / neural crest cell differentiation / inner ear morphogenesis / negative regulation of Wnt signaling pathway / positive regulation of fat cell differentiation / canonical Wnt signaling pathway / negative regulation of canonical Wnt signaling pathway / negative regulation of cell growth / positive regulation of apoptotic process / negative regulation of cell population proliferation / extracellular space / extracellular region / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Dann III, C.E. / Hsieh, J.C. / Rattner, A. / Sharma, D. / Nathans, J. / Leahy, D.J. | ||||||
![]() | ![]() Title: Insights into Wnt binding and signalling from the structures of two Frizzled cysteine-rich domains. Authors: Dann III, C.E. / Hsieh, J.C. / Rattner, A. / Sharma, D. / Nathans, J. / Leahy, D.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 157.5 KB | Display | ![]() |
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PDB format | ![]() | 132.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 485.8 KB | Display | ![]() |
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Full document | ![]() | 500.5 KB | Display | |
Data in XML | ![]() | 35.1 KB | Display | |
Data in CIF | ![]() | 49.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 14199.509 Da / Num. of mol.: 6 / Fragment: CYSTEINE-RICH DOMAIN / Mutation: N17E Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-SO4 / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.16 % | ||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.6 Details: PEG 3350, PEG 400, Sodium Hepes, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 11, 2000 |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9203 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→30 Å / Num. all: 61210 / Num. obs: 61070 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 26.3 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.679 / Mean I/σ(I) obs: 2.2 / Num. unique all: 6167 / % possible all: 98.7 |
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Processing
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Refinement | Method to determine structure: ![]()
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Refinement step | Cycle: LAST / Resolution: 1.9→30 Å
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 30 Å / σ(F): 0 / Rfactor obs: 0.22 / Rfactor Rwork: 0.22 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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