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Yorodumi- PDB-5ryy: EPB41L3 PanDDA analysis group deposition -- Crystal Structure of ... -
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-Basic information
Entry | Database: PDB / ID: 5ryy | ||||||
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Title | EPB41L3 PanDDA analysis group deposition -- Crystal Structure of the FERM domain of human EPB41L3 in complex with Z57257264 | ||||||
Components | Isoform 2 of Band 4.1-like protein 3 | ||||||
Keywords | CELL ADHESION / SGC - Diamond I04-1 fragment screening / PanDDA / XChemExplorer | ||||||
Function / homology | Function and homology information protein localization to paranode region of axon / cytoskeletal protein-membrane anchor activity / paranodal junction assembly / protein localization to juxtaparanode region of axon / myelin maintenance / paranode region of axon / cortical cytoskeleton organization / actomyosin structure organization / juxtaparanode region of axon / Neurexins and neuroligins ...protein localization to paranode region of axon / cytoskeletal protein-membrane anchor activity / paranodal junction assembly / protein localization to juxtaparanode region of axon / myelin maintenance / paranode region of axon / cortical cytoskeleton organization / actomyosin structure organization / juxtaparanode region of axon / Neurexins and neuroligins / Sensory processing of sound by outer hair cells of the cochlea / Sensory processing of sound by inner hair cells of the cochlea / cortical actin cytoskeleton organization / neuron projection morphogenesis / protein localization to plasma membrane / structural constituent of cytoskeleton / cell-cell junction / cell junction / actin binding / regulation of cell shape / cytoskeleton / apoptotic process / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 1.69 Å | ||||||
Authors | Bradshaw, W.J. / Katis, V.L. / Newman, J.A. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Gileadi, O. | ||||||
Citation | Journal: To Be Published Title: EPB41L3 PanDDA analysis group deposition Authors: Bradshaw, W.J. / Katis, V.L. / Newman, J.A. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Gileadi, O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ryy.cif.gz | 77.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ryy.ent.gz | 56.8 KB | Display | PDB format |
PDBx/mmJSON format | 5ryy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ry/5ryy ftp://data.pdbj.org/pub/pdb/validation_reports/ry/5ryy | HTTPS FTP |
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-Group deposition
ID | G_1002181 (51 entries) |
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Title | EPB41L3 PanDDA analysis group deposition |
Type | changed state |
Description | The FERM domain of HUMAN EPB41L3 screened against the Enamine DSI-poised fragment library by X-ray Crystallography at the XChem facility of Diamond Light Source beamline I04-1 |
-Related structure data
Related structure data | 6ibeS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 33395.305 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: EPB41L3, DAL1, KIAA0987 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y2J2 | ||||
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#2: Chemical | ChemComp-WGV / | ||||
#3: Chemical | ChemComp-DMS / | ||||
#4: Chemical | ChemComp-EDO / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.87 % / Mosaicity: 0 ° |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 0.075M ammonium nitrate, 0.1M MES pH 6.0, 6.5% PEG 2000, 6.5% PEG 3350, 6.5% PEG 4000, 6.5% PEG 5000, 10% ethylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å | |||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 12, 2019 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.91587 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 1.69→49.7 Å / Num. obs: 34308 / % possible obs: 99.9 % / Redundancy: 6.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.028 / Rrim(I) all: 0.072 / Net I/σ(I): 13.9 / Num. measured all: 218016 / Scaling rejects: 11 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Redundancy: 5.6 %
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 6IBE Resolution: 1.69→49.75 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.938 / SU B: 3.697 / SU ML: 0.115 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.162 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 89.01 Å2 / Biso mean: 33.27 Å2 / Biso min: 15.47 Å2
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Refinement step | Cycle: final / Resolution: 1.69→49.75 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.69→1.734 Å / Total num. of bins used: 20
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