+Open data
-Basic information
Entry | Database: PDB / ID: 7twd | ||||||
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Title | Structure of AAGAB C-terminal dimerization domain | ||||||
Components | Alpha- and gamma-adaptin-binding protein p34 | ||||||
Keywords | CHAPERONE / protein binding / membrane trafficking / AP Complex | ||||||
Function / homology | Alpha/gamma-adaptin-binding protein p34 / protein transport / nuclear speck / cytoplasm / cytosol / PHOSPHATE ION / Alpha- and gamma-adaptin-binding protein p34 Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.11 Å | ||||||
Authors | Tian, Y. / Yin, Q. | ||||||
Funding support | United States, 1items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2023 Title: Oligomer-to-monomer transition underlies the chaperone function of AAGAB in AP1/AP2 assembly. Authors: Tian, Y. / Datta, I. / Yang, R. / Wan, C. / Wang, B. / Crisman, L. / He, H. / Brautigam, C.A. / Li, S. / Shen, J. / Yin, Q. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7twd.cif.gz | 62.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7twd.ent.gz | 38.6 KB | Display | PDB format |
PDBx/mmJSON format | 7twd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7twd_validation.pdf.gz | 437.5 KB | Display | wwPDB validaton report |
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Full document | 7twd_full_validation.pdf.gz | 437.6 KB | Display | |
Data in XML | 7twd_validation.xml.gz | 6.7 KB | Display | |
Data in CIF | 7twd_validation.cif.gz | 8.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tw/7twd ftp://data.pdbj.org/pub/pdb/validation_reports/tw/7twd | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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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/peptide | Mass: 5184.021 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AAGAB / Production host: Escherichia coli (E. coli) / References: UniProt: Q6PD74 #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 3.01 Å3/Da / Density % sol: 59.15 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 30% glycerol, 0.5 M ammonium phosphate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 7, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 9351 / % possible obs: 99.2 % / Redundancy: 13.5 % / Biso Wilson estimate: 22.72 Å2 / CC1/2: 0.985 / CC star: 0.996 / Rmerge(I) obs: 0.205 / Rpim(I) all: 0.057 / Rrim(I) all: 0.213 / Χ2: 0.458 / Net I/σ(I): 17.4 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 9.6 % / Rmerge(I) obs: 1.58 / Mean I/σ(I) obs: 0.929 / Num. unique obs: 900 / CC1/2: 0.38 / CC star: 0.742 / Rpim(I) all: 0.479 / Rrim(I) all: 1.658 / Χ2: 0.458 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.11→40.25 Å / SU ML: 0.2164 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 23.4306 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.63 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.11→40.25 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -24.1235768997 Å / Origin y: 10.4592267274 Å / Origin z: -1.3874935756 Å
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Refinement TLS group | Selection details: all |