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- PDB-1gyv: Gamma-adaptin appendage domain from clathrin adaptor AP1, L762E mutant -
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Open data
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Basic information
Entry | Database: PDB / ID: 1gyv | ||||||
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Title | Gamma-adaptin appendage domain from clathrin adaptor AP1, L762E mutant | ||||||
![]() | ADAPTER-RELATED PROTEIN COMPLEX 1 GAMMA 1 SUBUNIT | ||||||
![]() | ENDOCYTOSIS / ADAPTOR / CLATHRIN / GOLGI / ADAPTIN | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Evans, P.R. / Owen, D.J. / McMahon, H.M. / Kent, H.M. | ||||||
![]() | ![]() Title: Gamma-adaptin appendage domain: structure and binding site for Eps15 and gamma-synergin. Authors: Kent, H.M. / McMahon, H.T. / Evans, P.R. / Benmerah, A. / Owen, D.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 41.6 KB | Display | ![]() |
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PDB format | ![]() | 27.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 423.2 KB | Display | ![]() |
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Full document | ![]() | 425 KB | Display | |
Data in XML | ![]() | 9.2 KB | Display | |
Data in CIF | ![]() | 13.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1gyuSC ![]() 1gywC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 13433.230 Da / Num. of mol.: 1 / Fragment: APPENDAGE DOMAIN, RESIDUES 703-821 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47.02 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 15, 2000 / Details: OSMIC |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54182 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→18.7 Å / Num. obs: 14209 / % possible obs: 99.6 % / Observed criterion σ(I): 6 / Redundancy: 6.4 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 22 |
Reflection shell | Resolution: 1.7→1.8 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.279 / Mean I/σ(I) obs: 6 / % possible all: 97.9 |
Reflection shell | *PLUS % possible obs: 97.9 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1GYU Resolution: 1.71→42.64 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.933 / SU B: 3.005 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.116 / ESU R Free: 0.118 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.94 Å2
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Refinement step | Cycle: LAST / Resolution: 1.71→42.64 Å
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Refine LS restraints |
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