+Open data
-Basic information
Entry | Database: PDB / ID: 1i0c | ||||||
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Title | EPS8 SH3 CLOSED MONOMER | ||||||
Components | EPIDERMAL GROWTH FACTOR RECEPTOR KINASE SUBSTRATE EPS8 | ||||||
Keywords | HORMONE/GROWTH FACTOR / HORMONE-GROWTH FACTOR complex | ||||||
Function / homology | Function and homology information regulation of actin filament length / actin polymerization-dependent cell motility / dendritic cell migration / stereocilium tip / actin crosslink formation / stereocilium bundle / behavioral response to ethanol / stereocilium / regulation of Rho protein signal transduction / exit from mitosis ...regulation of actin filament length / actin polymerization-dependent cell motility / dendritic cell migration / stereocilium tip / actin crosslink formation / stereocilium bundle / behavioral response to ethanol / stereocilium / regulation of Rho protein signal transduction / exit from mitosis / barbed-end actin filament capping / positive regulation of ruffle assembly / NMDA selective glutamate receptor complex / Rac protein signal transduction / regulation of postsynaptic membrane neurotransmitter receptor levels / actin filament bundle assembly / brush border / Rho protein signal transduction / adult locomotory behavior / cellular response to leukemia inhibitory factor / small GTPase binding / ruffle membrane / actin binding / cell cortex / regulation of cell shape / growth cone / actin cytoskeleton organization / postsynaptic density / glutamatergic synapse / synapse / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Kishan, K.V.R. / Newcomer, M.E. | ||||||
Citation | Journal: Protein Sci. / Year: 2001 Title: Effect of pH and salt bridges on structural assembly: molecular structures of the monomer and intertwined dimer of the Eps8 SH3 domain. Authors: Kishan, K.V. / Newcomer, M.E. / Rhodes, T.H. / Guilliot, S.D. #1: Journal: Nat.Struct.Biol. / Year: 1997 Title: The sh3 domain of eps8 exists as a novel intertwined dimer. Authors: Kishan, K.V. / Scita, G. / Wong, W.T. / Di Fiore, P.P. / Newcomer, M.E. | ||||||
History |
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Remark 300 | BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). THE BIOLOGICAL UNIT IS A MONOMER. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1i0c.cif.gz | 37.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1i0c.ent.gz | 25.5 KB | Display | PDB format |
PDBx/mmJSON format | 1i0c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i0/1i0c ftp://data.pdbj.org/pub/pdb/validation_reports/i0/1i0c | HTTPS FTP |
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-Related structure data
Related structure data | 1i07C 1aojS C: citing same article (ref.) 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 7044.960 Da / Num. of mol.: 2 / Fragment: SH3 DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: Q08509 #2: Water | ChemComp-HOH / | |
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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: 1.85 Å3/Da / Density % sol: 33.42 % | |||||||||||||||||||||||||
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Crystal grow | pH: 4 / Details: pH 4.0 | |||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2→21.54 Å / Num. all: 6799 / Num. obs: 6795 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 13.1 Å2 / Limit h max: 21 / Limit h min: -20 / Limit k max: 24 / Limit k min: -20 / Limit l max: 18 / Limit l min: 0 / Observed criterion F max: 318300.17 / Observed criterion F min: 0.55 / Rmerge(I) obs: 0.069 |
Reflection | *PLUS % possible obs: 99.7 % / Num. measured all: 24299 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1AOJ Resolution: 2→22 Å / Rfactor Rfree error: 0.009 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: engh & huber
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Solvent computation | Solvent model: CNS bulk solvent model used / Bsol: 40.1813 Å2 / ksol: 0.342613 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 58.2 Å2 / Biso mean: 25.6 Å2 / Biso min: 12.69 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→22 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.5 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 22 Å / σ(F): 0 / % reflection Rfree: 10.9 % / Rfactor obs: 0.189 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.232 / % reflection Rfree: 10.4 % / Rfactor Rwork: 0.235 |