+Open data
-Basic information
Entry | Database: PDB / ID: 6ibe | ||||||
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Title | The FERM domain of Human EPB41L3 | ||||||
Components | Band 4.1-like protein 3 | ||||||
Keywords | CELL ADHESION / Ferm domain / Alzheimer's Disease | ||||||
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 inner hair cells of the cochlea / Sensory processing of sound by outer 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 / MOLECULAR REPLACEMENT / Resolution: 1.45 Å | ||||||
Authors | Bradshaw, W.J. / Katis, V.L. / Newman, J.A. / Fernandez-Cid, A. / Burgess-Brown, N. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Gileadi, O. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: The FERM domain of Human EPB41L3 Authors: Bradshaw, W.J. / Katis, V.L. / Newman, J.A. / Fernandez-Cid, A. / Burgess-Brown, N. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / 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 | 6ibe.cif.gz | 147.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ibe.ent.gz | 115.4 KB | Display | PDB format |
PDBx/mmJSON format | 6ibe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ib/6ibe ftp://data.pdbj.org/pub/pdb/validation_reports/ib/6ibe | HTTPS FTP |
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-Related structure data
Related structure data | 2he7S 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 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y2J2 | ||||
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#2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-MES / | #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: 2.27 Å3/Da / Density % sol: 45.79 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 0.15 M ammonium nitrate, 0.1 M MES, 5% (v/v) ethylene glycol, 5% (w/v) PEG 2000, 5% (w/v) PEG 3350, 5% (w/v) PEG 4000, 5% (w/v) PEG 5000 MME |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 5, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→78.69 Å / Num. obs: 54827 / % possible obs: 100 % / Redundancy: 6.1 % / CC1/2: 0.944 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.043 / Rrim(I) all: 0.079 / Χ2: 0.81 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 1.45→1.48 Å / Redundancy: 5.4 % / Rmerge(I) obs: 1.536 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2741 / CC1/2: 0.401 / Rpim(I) all: 1.098 / Rrim(I) all: 1.896 / Χ2: 0.5 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2HE7 Resolution: 1.45→61.59 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.926 / SU ML: 0.049 / Cross valid method: THROUGHOUT / ESU R: 0.07 / ESU R Free: 0.067 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.261 Å2
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Refinement step | Cycle: 1 / Resolution: 1.45→61.59 Å
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Refine LS restraints |
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