+Open data
-Basic information
Entry | Database: PDB / ID: 1gyu | ||||||
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Title | Gamma-adaptin appendage domain from clathrin adaptor AP1 | ||||||
Components | ADAPTER-RELATED PROTEIN COMPLEX 1 GAMMA 1 SUBUNIT | ||||||
Keywords | ENDOCYTOSIS / CLATHRIN / GOLGI / ADAPTIN / ADAPTOR | ||||||
Function / homology | Function and homology information basolateral protein secretion / AP-1 adaptor complex / Lysosome Vesicle Biogenesis / platelet dense granule organization / melanosome assembly / Golgi to vacuole transport / Golgi Associated Vesicle Biogenesis / clathrin adaptor activity / MHC class II antigen presentation / clathrin-coated vesicle ...basolateral protein secretion / AP-1 adaptor complex / Lysosome Vesicle Biogenesis / platelet dense granule organization / melanosome assembly / Golgi to vacuole transport / Golgi Associated Vesicle Biogenesis / clathrin adaptor activity / MHC class II antigen presentation / clathrin-coated vesicle / clathrin-coated pit / vesicle-mediated transport / trans-Golgi network membrane / intracellular protein transport / trans-Golgi network / early endosome / lysosomal membrane / perinuclear region of cytoplasm Similarity search - Function | ||||||
Biological species | MUS MUSCULUS (house mouse) | ||||||
Method | X-RAY DIFFRACTION / MIR / Resolution: 1.81 Å | ||||||
Authors | Evans, P.R. / Owen, D.J. / McMahon, H.M. / Kent, H.M. | ||||||
Citation | Journal: Structure / Year: 2002 Title: Gamma-Adaptin Appendage Domain. Structure and Binding Site for Eps15 and Gamma-Synergin Authors: Kent, H.M. / Mcmahon, H.M. / Evans, P.R. / Benmerah, A. / Owen, D.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1gyu.cif.gz | 40.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gyu.ent.gz | 27.9 KB | Display | PDB format |
PDBx/mmJSON format | 1gyu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gy/1gyu ftp://data.pdbj.org/pub/pdb/validation_reports/gy/1gyu | 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
#1: Protein | Mass: 15588.646 Da / Num. of mol.: 1 / Fragment: APPENDAGE DOMAIN, RESIDUES 703-821 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PET15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P22892 |
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#2: Water | ChemComp-HOH / |
Sequence details | LEADER IS HIS6-TAG CLONING ARTIFACT |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.66 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.4 Details: 50MM HEPES PH7.4, 0.9M NA/K TARTRATE, 20% W/V GLYCEROL, pH 7.40 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: ELLIOTT GX-13 / Wavelength: 1.54182 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 15, 1998 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54182 Å / Relative weight: 1 |
Reflection | Resolution: 1.81→26 Å / Num. obs: 11924 / % possible obs: 98.7 % / Observed criterion σ(I): 6 / Redundancy: 3.7 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 15 |
Reflection shell | Resolution: 1.81→1.91 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.242 / Mean I/σ(I) obs: 5 / % possible all: 92.2 |
Reflection | *PLUS Lowest resolution: 26 Å / Rmerge(I) obs: 0.062 |
Reflection shell | *PLUS % possible obs: 92.2 % / Mean I/σ(I) obs: 5.1 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 1.81→42.64 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.934 / SU B: 3.681 / SU ML: 0.115 / Cross valid method: THROUGHOUT / ESU R: 0.138 / ESU R Free: 0.135 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES 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: 18.04 Å2
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Refinement step | Cycle: LAST / Resolution: 1.81→42.64 Å
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Refine LS restraints |
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