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Yorodumi- PDB-6g8t: Crystal Structures of the Single PDZ Domains from GRASP65 and the... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6g8t | ||||||
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Title | Crystal Structures of the Single PDZ Domains from GRASP65 and their Interaction with the Golgin GM130 | ||||||
Components | Golgi reassembly-stacking protein 1 | ||||||
Keywords | PROTEIN BINDING / PDZ1 domain structure / Golgi stacking / GRASP family / Golgins / Golgi apparatus / yeast homolog of GRASP65 / vesicle transport | ||||||
Function / homology | Function and homology information establishment of protein localization to plasma membrane / negative regulation of dendrite morphogenesis / Golgi ribbon formation / cis-Golgi network / protein N-linked glycosylation / Golgi Cisternae Pericentriolar Stack Reorganization / COPII-mediated vesicle transport / Golgi organization / COPI-mediated anterograde transport / endoplasmic reticulum-Golgi intermediate compartment membrane ...establishment of protein localization to plasma membrane / negative regulation of dendrite morphogenesis / Golgi ribbon formation / cis-Golgi network / protein N-linked glycosylation / Golgi Cisternae Pericentriolar Stack Reorganization / COPII-mediated vesicle transport / Golgi organization / COPI-mediated anterograde transport / endoplasmic reticulum-Golgi intermediate compartment membrane / protein transport / Golgi membrane / Golgi apparatus / metal ion binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.67 Å | ||||||
Authors | Jurk, C.M. / Roske, Y. / Heinemann, U. | ||||||
Citation | Journal: Croatica Chemica Acta / Year: 2018 Title: Crystal Structures of the Single PDZ Domains from GRASP65 and their Interaction with the Golgin GM130 Authors: Jurk, C.M. / Roske, Y. / Heinemann, U. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6g8t.cif.gz | 35.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6g8t.ent.gz | 22.7 KB | Display | PDB format |
PDBx/mmJSON format | 6g8t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g8/6g8t ftp://data.pdbj.org/pub/pdb/validation_reports/g8/6g8t | HTTPS FTP |
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-Related structure data
Related structure data | 6g8wC 6g8yC 3rleS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-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: 13020.861 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GORASP1, GOLPH5, GRASP65 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BQQ3 |
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#2: Chemical | ChemComp-GOL / |
#3: 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: 2.27 Å3/Da / Density % sol: 45.87 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 24% PEG1500, 20% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 15, 2011 |
Radiation | Monochromator: KMC-1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 2.67→33.93 Å / Num. obs: 3573 / % possible obs: 99.8 % / Redundancy: 4.3 % / CC1/2: 0.99 / Rrim(I) all: 0.062 / Net I/σ(I): 20.67 |
Reflection shell | Resolution: 2.67→2.74 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 2.28 / Num. unique obs: 260 / CC1/2: 0.7 / Rrim(I) all: 0.75 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3RLE Resolution: 2.67→33.93 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.921 / SU B: 10.657 / SU ML: 0.227 / Cross valid method: THROUGHOUT / ESU R Free: 0.075 / 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: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 62.112 Å2
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Refinement step | Cycle: 1 / Resolution: 2.67→33.93 Å
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