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Yorodumi- PDB-2oei: Crystal structure of human FE65-WW domain in complex with human M... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2oei | ||||||
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Title | Crystal structure of human FE65-WW domain in complex with human Mena peptide | ||||||
Components |
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Keywords | PROTEIN BINDING / WW domain / FE65 / human Mena | ||||||
Function / homology | Function and homology information negative regulation of cell cycle G1/S phase transition / proline-rich region binding / low-density lipoprotein particle receptor binding / smooth muscle contraction / axonogenesis / positive regulation of protein secretion / positive regulation of neuron projection development / lamellipodium / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromatin organization ...negative regulation of cell cycle G1/S phase transition / proline-rich region binding / low-density lipoprotein particle receptor binding / smooth muscle contraction / axonogenesis / positive regulation of protein secretion / positive regulation of neuron projection development / lamellipodium / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromatin organization / amyloid-beta binding / growth cone / histone binding / transcription coactivator activity / molecular adaptor activity / nuclear speck / positive regulation of apoptotic process / synapse / apoptotic process / DNA damage response / ubiquitin protein ligase binding / chromatin binding / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / signal transduction / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å | ||||||
Authors | Meiyappan, M. / Birrane, G. / Ladias, J.A.A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 Title: Structural Basis for Polyproline Recognition by the FE65 WW Domain. Authors: Meiyappan, M. / Birrane, G. / Ladias, J.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2oei.cif.gz | 31.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2oei.ent.gz | 21.3 KB | Display | PDB format |
PDBx/mmJSON format | 2oei.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oe/2oei ftp://data.pdbj.org/pub/pdb/validation_reports/oe/2oei | 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/peptide | Mass: 4194.533 Da / Num. of mol.: 1 / Fragment: WW domain (residues 253-289) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: APBB1, FE65 / Plasmid: PGEX-KT / Production host: Escherichia coli (E. coli) / References: UniProt: O00213 |
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#2: Protein/peptide | Mass: 908.091 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: The peptide was chemically synthesized. The sequence of the peptide can be naturally found in Homo sapiens (Human). |
#3: 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: 2.56 Å3/Da / Density % sol: 51.87 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.6 Details: 1.3 M sodium citrate, 0.1M hepes, pH 7.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 1 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 19, 2006 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.27→50 Å / Num. all: 14732 / Num. obs: 14379 / % possible obs: 97.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.5 % / Rmerge(I) obs: 0.044 / Rsym value: 0.036 / Net I/σ(I): 21.4 |
Reflection shell | Resolution: 1.27→1.32 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.386 / % possible all: 93.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.35→25.77 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.945 / SU B: 1.658 / SU ML: 0.031 / Cross valid method: THROUGHOUT / ESU R: 0.06 / ESU R Free: 0.058 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.119 Å2
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Refinement step | Cycle: LAST / Resolution: 1.35→25.77 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.35→1.385 Å / Total num. of bins used: 20
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