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Yorodumi- PDB-3fia: Crystal structure of the EH 1 domain from human intersectin-1 pro... -
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-Basic information
Entry | Database: PDB / ID: 3fia | ||||||
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Title | Crystal structure of the EH 1 domain from human intersectin-1 protein. Northeast Structural Genomics Consortium target HR3646e. | ||||||
Components | Intersectin-1 | ||||||
Keywords | PROTEIN BINDING / Intersectin-1 / EH 1 domain / NESG / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / Alternative splicing / Calcium / Cell junction / Cell projection / Coiled coil / Endocytosis / Membrane / Phosphoprotein / SH3 domain / Synapse / Synaptosome | ||||||
Function / homology | Function and homology information clathrin-dependent synaptic vesicle endocytosis / proline-rich region binding / regulation of small GTPase mediated signal transduction / endosomal transport / intracellular vesicle / NRAGE signals death through JNK / RHOQ GTPase cycle / exocytosis / CDC42 GTPase cycle / RHOG GTPase cycle ...clathrin-dependent synaptic vesicle endocytosis / proline-rich region binding / regulation of small GTPase mediated signal transduction / endosomal transport / intracellular vesicle / NRAGE signals death through JNK / RHOQ GTPase cycle / exocytosis / CDC42 GTPase cycle / RHOG GTPase cycle / clathrin-coated pit / EPHB-mediated forward signaling / guanyl-nucleotide exchange factor activity / protein localization / recycling endosome / G alpha (12/13) signalling events / protein transport / Cargo recognition for clathrin-mediated endocytosis / lamellipodium / presynaptic membrane / Clathrin-mediated endocytosis / nuclear envelope / molecular adaptor activity / neuron projection / intracellular signal transduction / calcium ion binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.45 Å | ||||||
Authors | Vorobiev, S.M. / Chen, Y. / Seetharaman, J. / Devices, C. / Zhao, L. / Foote, E.L. / Ciccosanti, C. / Mao, L. / Xiao, R. / Acton, T.B. ...Vorobiev, S.M. / Chen, Y. / Seetharaman, J. / Devices, C. / Zhao, L. / Foote, E.L. / Ciccosanti, C. / Mao, L. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: To be Published Title: Crystal structure of the EH 1 domain from human intersectin-1 protein. Authors: Vorobiev, S.M. / Chen, Y. / Seetharaman, J. / Devices, C. / Zhao, L. / Foote, E.L. / Ciccosanti, C. / Mao, L. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3fia.cif.gz | 55.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3fia.ent.gz | 43 KB | Display | PDB format |
PDBx/mmJSON format | 3fia.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fi/3fia ftp://data.pdbj.org/pub/pdb/validation_reports/fi/3fia | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | monomer according to aggregation screening |
-Components
#1: Protein | Mass: 13816.960 Da / Num. of mol.: 1 / Fragment: residues 1-111 / Mutation: M1V, I14T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ITSN, ITSN1, SH3D1A / Plasmid: pET 14-15c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) +Magic / References: UniProt: Q15811 |
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#2: Chemical | ChemComp-CA / |
#3: Chemical | ChemComp-SO4 / |
#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: 1.75 Å3/Da / Density % sol: 29.89 % |
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Crystal grow | Temperature: 277 K / Method: microbatch under oil / pH: 8.5 Details: 1.5M ammonium sulfate, 12% glycerol, 0.1M TrisHCl, pH 8.5, microbatch under oil , temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97869 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Dec 5, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97869 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→50 Å / Num. all: 33173 / Num. obs: 31879 / % possible obs: 96.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 33.75 |
Reflection shell | Resolution: 1.45→1.5 Å / Redundancy: 3 % / Rmerge(I) obs: 0.222 / Mean I/σ(I) obs: 4.9 / Num. unique all: 3311 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.45→45.5 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.427 / SU ML: 0.027 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.08 / ESU R Free: 0.062 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.003 Å2
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Refinement step | Cycle: LAST / Resolution: 1.45→45.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.451→1.489 Å / Total num. of bins used: 20
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