+Open data
-Basic information
Entry | Database: PDB / ID: 1jwf | ||||||
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Title | Crystal Structure of human GGA1 VHS domain. | ||||||
Components | ADP-ribosylation factor binding protein GGA1 | ||||||
Keywords | PROTEIN TRANSPORT / Super Helix | ||||||
Function / homology | Function and homology information protein localization to ciliary membrane / Golgi to plasma membrane transport / Golgi to plasma membrane protein transport / retrograde transport, endosome to Golgi / protein localization to cell surface / TBC/RABGAPs / phosphatidylinositol binding / ubiquitin binding / intracellular protein transport / trans-Golgi network ...protein localization to ciliary membrane / Golgi to plasma membrane transport / Golgi to plasma membrane protein transport / retrograde transport, endosome to Golgi / protein localization to cell surface / TBC/RABGAPs / phosphatidylinositol binding / ubiquitin binding / intracellular protein transport / trans-Golgi network / protein catabolic process / small GTPase binding / positive regulation of protein catabolic process / protein localization / early endosome membrane / endosome membrane / early endosome / Amyloid fiber formation / intracellular membrane-bounded organelle / Golgi apparatus / protein-containing complex / nucleoplasm / membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Shiba, T. / Takatsu, H. / Nogi, T. / Matsugaki, N. / Kawasaki, M. / Igarashi, N. / Suzuki, M. / Kato, R. / Earnest, T. / Nakayama, K. / Wakatsuki, S. | ||||||
Citation | Journal: Nature / Year: 2002 Title: Structural basis for recognition of acidic-cluster dileucine sequence by GGA1. Authors: Shiba, T. / Takatsu, H. / Nogi, T. / Matsugaki, N. / Kawasaki, M. / Igarashi, N. / Suzuki, M. / Kato, R. / Earnest, T. / Nakayama, K. / Wakatsuki, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jwf.cif.gz | 35.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jwf.ent.gz | 28.2 KB | Display | PDB format |
PDBx/mmJSON format | 1jwf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1jwf_validation.pdf.gz | 370.4 KB | Display | wwPDB validaton report |
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Full document | 1jwf_full_validation.pdf.gz | 372 KB | Display | |
Data in XML | 1jwf_validation.xml.gz | 4.3 KB | Display | |
Data in CIF | 1jwf_validation.cif.gz | 6.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jw/1jwf ftp://data.pdbj.org/pub/pdb/validation_reports/jw/1jwf | HTTPS FTP |
-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: 16814.436 Da / Num. of mol.: 1 / Fragment: VHS DOMAIN(N-terminal domain) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pgex4t-2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UJY5 |
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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: 2.38 Å3/Da / Density % sol: 48.36 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG 3350, potassium dihydrogen phosphate, Tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8 | ||||||||||||||||||||||||||||||||||||
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: Photon Factory / Beamline: BL-6B / Wavelength: 1 Å |
Detector | Type: FUJI / Detector: IMAGE PLATE / Date: May 29, 2001 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→15 Å / Num. all: 9057 / Num. obs: 39125 / % possible obs: 95.6 % |
Reflection shell | Resolution: 2.1→2.17 Å / % possible all: 89.4 |
Reflection | *PLUS Num. obs: 9580 / Num. measured all: 39125 / Rmerge(I) obs: 0.044 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→15 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.916 / SU B: 5.885 / SU ML: 0.157 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.245 / ESU R Free: 0.202 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 34.401 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.153 Å / Total num. of bins used: 20
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Refinement | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 15 Å / σ(F): 0 / % reflection Rfree: 4.8 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 2.15 Å / Rfactor Rfree: 0.319 / Rfactor Rwork: 0.244 |