+Open data
-Basic information
Entry | Database: PDB / ID: 1uru | ||||||
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Title | Amphiphysin BAR domain from Drosophila | ||||||
Components | AMPHIPHYSIN | ||||||
Keywords | ENDOCYTOSIS / COILED-COIL / MEMBRANE CURVATURE | ||||||
Function / homology | Function and homology information rhabdomere membrane biogenesis / organelle / rhabdomere development / Clathrin-mediated endocytosis / Neutrophil degranulation / regulation of muscle contraction / exocytosis / cleavage furrow / protein localization / phospholipid binding ...rhabdomere membrane biogenesis / organelle / rhabdomere development / Clathrin-mediated endocytosis / Neutrophil degranulation / regulation of muscle contraction / exocytosis / cleavage furrow / protein localization / phospholipid binding / synapse / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | DROSOPHILA MELANOGASTER (fruit fly) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.6 Å | ||||||
Authors | Evans, P.R. / Kent, H.M. | ||||||
Citation | Journal: Science / Year: 2004 Title: Bar Domains as Sensors of Membrane Curvature: The Amphiphysin Bar Structure Authors: Peter, B.J. / Kent, H.M. / Mills, I.G. / Vallis, Y. / Butler, J.G. / 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 | 1uru.cif.gz | 52.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1uru.ent.gz | 41.7 KB | Display | PDB format |
PDBx/mmJSON format | 1uru.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1uru_validation.pdf.gz | 425.3 KB | Display | wwPDB validaton report |
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Full document | 1uru_full_validation.pdf.gz | 429 KB | Display | |
Data in XML | 1uru_validation.xml.gz | 10.3 KB | Display | |
Data in CIF | 1uru_validation.cif.gz | 13.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ur/1uru ftp://data.pdbj.org/pub/pdb/validation_reports/ur/1uru | 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 28269.152 Da / Num. of mol.: 1 / Fragment: BAR DOMAIN, RESIDUES 1-244 Source method: isolated from a genetically manipulated source Details: SEMET SUBSTITUTED / Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Description: GROWN IN MINIMAL MEDIUM + SEMET / Plasmid: PGEX / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q9Y092, UniProt: Q7KLE5*PLUS |
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#2: 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: 2.39 Å3/Da / Density % sol: 51.1 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion / pH: 6 Details: 2.5MG/ML PROTEIN SOLUTION IN 18% PEG4000, 200MM NACL, 1MM DTT, 20MM HEPES PH 7.4 MIXED WITH THE WELL SOLUTION 18% PEG 4000, 0.2M AMMONIUM ACETATE, 100MM SODIUM CITRATE PH 6.0. CRYSTALS WERE ...Details: 2.5MG/ML PROTEIN SOLUTION IN 18% PEG4000, 200MM NACL, 1MM DTT, 20MM HEPES PH 7.4 MIXED WITH THE WELL SOLUTION 18% PEG 4000, 0.2M AMMONIUM ACETATE, 100MM SODIUM CITRATE PH 6.0. CRYSTALS WERE EQUILIBRATED IN 20% GLYCEROL FOR COOLING TO 100K. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.4 / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Nov 15, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→31.94 Å / Num. obs: 8657 / % possible obs: 97.2 % / Redundancy: 10.21 % / Rmerge(I) obs: 0.134 / Net I/σ(I): 4.9102 |
Reflection shell | Resolution: 2.6→2.74 Å / Redundancy: 9.29 % / Rmerge(I) obs: 1.01 / Mean I/σ(I) obs: 0.73 / % possible all: 86 |
Reflection shell | *PLUS % possible obs: 86 % / Rmerge(I) obs: 0.01005 / Mean I/σ(I) obs: 2.7 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER / Resolution: 2.6→63.25 Å / SU B: 13.987 / SU ML: 0.283 / Cross valid method: THROUGHOUT / ESU R: 1.164 / ESU R Free: 0.402
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Displacement parameters | Biso mean: 55.997 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→63.25 Å
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Rfactor all: 0.23405 / Rfactor obs: 0.23 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS Type: p_bond_d / Dev ideal: 0.013 |