+Open data
-Basic information
Entry | Database: PDB / ID: 1bb9 | ||||||
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Title | CRYSTAL STRUCTURE OF THE SH3 DOMAIN FROM RAT AMPHIPHYSIN 2 | ||||||
Components | AMPHIPHYSIN 2 | ||||||
Keywords | TRANSFERASE / SH3 DOMAIN | ||||||
Function / homology | Function and homology information regulation of cell cycle => GO:0051726 / lipid tube / negative regulation of ventricular cardiac muscle cell action potential / negative regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / negative regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process / lipid tube assembly / T-tubule organization / negative regulation of potassium ion transmembrane transport / varicosity / extrinsic component of synaptic vesicle membrane ...regulation of cell cycle => GO:0051726 / lipid tube / negative regulation of ventricular cardiac muscle cell action potential / negative regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / negative regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process / lipid tube assembly / T-tubule organization / negative regulation of potassium ion transmembrane transport / varicosity / extrinsic component of synaptic vesicle membrane / nucleus localization / cerebellar mossy fiber / axon initial segment / Clathrin-mediated endocytosis / muscle cell differentiation / positive regulation of astrocyte differentiation / aspartic-type endopeptidase inhibitor activity / node of Ranvier / I band / RNA polymerase binding / regulation of neuron differentiation / positive regulation of actin filament polymerization / nucleus organization / endosome to lysosome transport / regulation of heart rate by cardiac conduction / negative regulation of amyloid-beta formation / positive regulation of endocytosis / synaptic vesicle endocytosis / axon terminus / T-tubule / positive regulation of GTPase activity / tau protein binding / phospholipid binding / Z disc / actin filament binding / synaptic vesicle / GTPase binding / nuclear envelope / protein-folding chaperone binding / microtubule / protease binding / endosome / positive regulation of apoptotic process / axon / glutamatergic synapse / synapse / protein-containing complex binding / identical protein binding / membrane / nucleus / plasma membrane Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIR / Resolution: 2.2 Å | ||||||
Authors | Owen, D.J. / Mcmahon, H.T. / Evans, P.R. | ||||||
Citation | Journal: EMBO J. / Year: 1998 Title: Crystal structure of the amphiphysin-2 SH3 domain and its role in the prevention of dynamin ring formation. Authors: Owen, D.J. / Wigge, P. / Vallis, Y. / Moore, J.D. / Evans, P.R. / McMahon, H.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1bb9.cif.gz | 31.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bb9.ent.gz | 20.1 KB | Display | PDB format |
PDBx/mmJSON format | 1bb9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1bb9_validation.pdf.gz | 431.9 KB | Display | wwPDB validaton report |
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Full document | 1bb9_full_validation.pdf.gz | 433 KB | Display | |
Data in XML | 1bb9_validation.xml.gz | 6.7 KB | Display | |
Data in CIF | 1bb9_validation.cif.gz | 8.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bb/1bb9 ftp://data.pdbj.org/pub/pdb/validation_reports/bb/1bb9 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 12879.215 Da / Num. of mol.: 1 / Fragment: SH3 DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Organ: BRAIN / Plasmid: PET15B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: O08839 |
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#2: Water | ChemComp-HOH / |
Compound details | THIS IS THE SH3 DOMAIN AT THE C-TERMINUS OF AMPHIPHYSIN-2. THIS DOMAIN BINDS TO THE PROLINE-RICH C- ...THIS IS THE SH3 DOMAIN AT THE C-TERMINUS OF AMPHIPHYSI |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.95 % Description: NATIVE DATA WERE MERGED FROM 2 CRYSTALS, ONE SET TO 2.2 ANGSTROM RESOLUTION COLLECTED ON THE SRS SYNCHROTRON PX9.5, THE OTHER COLLECTED TO 3.5 ANGSTROMS WAS COLLECTED ON A ROTATING ANODE. | |||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion / pH: 6 Details: VAPOUR DIFFUSION, PROTEIN 30MG/ML, RESERVOIR 2.0M AMMONIUM SULFATE, 100MM NA CITRATE PH6.0, PLUS 2MM DTT., vapor diffusion | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 16 ℃ / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.5 / Wavelength: 0.9 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 1, 1997 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→36 Å / Num. obs: 5401 / % possible obs: 99 % / Observed criterion σ(I): 6 / Redundancy: 4.2 % / Biso Wilson estimate: 35 Å2 / Rmerge(I) obs: 0.093 / Rsym value: 0.093 / Net I/σ(I): 4.7 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.201 / Mean I/σ(I) obs: 3.4 / Rsym value: 0.201 / % possible all: 99 |
Reflection | *PLUS % possible obs: 99.2 % |
Reflection shell | *PLUS % possible obs: 99.7 % |
-Processing
Software |
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Refinement | Method to determine structure: SIR / Resolution: 2.2→36 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 39 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati sigma a obs: 0.24 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→36 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.19 / Rfactor Rfree: 0.258 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |