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Yorodumi- PDB-8qpx: Crystal structure of Geodia cydonium Immunoglobulin-like domain o... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8qpx | |||||||||
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Title | Crystal structure of Geodia cydonium Immunoglobulin-like domain of Receptor Tyrosine Kinase | |||||||||
Components | Receptor tyrosine kinase (Fragment) | |||||||||
Keywords | IMMUNE SYSTEM / Ig-like / porifera / evolution | |||||||||
Function / homology | Function and homology information phosphorylation / cell adhesion molecule binding / cell-cell adhesion / cell-cell junction / kinase activity / plasma membrane Similarity search - Function | |||||||||
Biological species | Geodia cydonium (invertebrata) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | |||||||||
Authors | Lopez-Sagaseta, J. / Urdiciain, A. | |||||||||
Funding support | Spain, 2items
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Citation | Journal: To Be Published Title: Crystal structure of Geodia cydonium Immunoglobulin-like domain of Receptor Tyrosine Kinase Authors: Lopez-Sagaseta, J. / Urdiciain, A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8qpx.cif.gz | 115.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8qpx.ent.gz | 72.4 KB | Display | PDB format |
PDBx/mmJSON format | 8qpx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8qpx_validation.pdf.gz | 869 KB | Display | wwPDB validaton report |
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Full document | 8qpx_full_validation.pdf.gz | 869.8 KB | Display | |
Data in XML | 8qpx_validation.xml.gz | 10.9 KB | Display | |
Data in CIF | 8qpx_validation.cif.gz | 14.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qp/8qpx ftp://data.pdbj.org/pub/pdb/validation_reports/qp/8qpx | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 24623.100 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Remaining N-terminal GP motif from 3C site / Source: (gene. exp.) Geodia cydonium (invertebrata) / Gene: TK_2L / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O18431 |
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-Sugars , 2 types, 2 molecules
#2: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#3: Sugar | ChemComp-NAG / |
-Non-polymers , 3 types, 105 molecules
#4: Chemical | ChemComp-EDO / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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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: 2.5 Å3/Da / Density % sol: 50.85 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Ammonium sulfate, 26% w/v PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 22, 2023 |
Radiation | Monochromator: Si(111) channel cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97926 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→40.91 Å / Num. obs: 47524 / % possible obs: 98.6 % / Redundancy: 3.3 % / Biso Wilson estimate: 34.44 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.035 / Rpim(I) all: 0.023 / Χ2: 0.9 / Net I/σ(I): 17.4 |
Reflection shell | Resolution: 2.1→2.16 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.247 / Mean I/σ(I) obs: 5 / Num. unique obs: 3990 / CC1/2: 0.947 / Rpim(I) all: 0.157 / Χ2: 1 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→40.91 Å / SU ML: 0.2881 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.6235 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.41 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→40.91 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: 9.31014388062 Å / Origin y: -9.79483222786 Å / Origin z: 6.9598198259 Å
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Refinement TLS group | Selection details: (chain A and resseq 134:407) |