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Yorodumi- PDB-1r4a: Crystal Structure of GTP-bound ADP-ribosylation Factor Like Prote... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1r4a | ||||||
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Title | Crystal Structure of GTP-bound ADP-ribosylation Factor Like Protein 1 (Arl1) and GRIP Domain of Golgin245 COMPLEX | ||||||
Components |
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Keywords | PROTEIN TRANSPORT / Ras-like G Protein structure / Three-helix GRIP domain | ||||||
Function / homology | Function and homology information Retrograde transport at the Trans-Golgi-Network / activation of phospholipase D activity / toxin metabolic process / Retrograde transport at the Trans-Golgi-Network / Golgi vesicle transport / Signaling by membrane-tethered fusions of PDGFRA or PDGFRB / protein localization to Golgi apparatus / Golgi to plasma membrane protein transport / retrograde transport, endosome to Golgi / Golgi organization ...Retrograde transport at the Trans-Golgi-Network / activation of phospholipase D activity / toxin metabolic process / Retrograde transport at the Trans-Golgi-Network / Golgi vesicle transport / Signaling by membrane-tethered fusions of PDGFRA or PDGFRB / protein localization to Golgi apparatus / Golgi to plasma membrane protein transport / retrograde transport, endosome to Golgi / Golgi organization / enzyme activator activity / positive regulation of axon extension / vesicle-mediated transport / intracellular protein transport / trans-Golgi network / small GTPase binding / GTPase binding / protein domain specific binding / Golgi membrane / GTPase activity / GTP binding / Golgi apparatus / extracellular exosome / nucleoplasm / metal ion binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Wu, M. / Lu, L. / Hong, W. / Song, H. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2004 Title: Structural basis for recruitment of GRIP domain golgin-245 by small GTPase Arl1. Authors: Wu, M. / Lu, L. / Hong, W. / Song, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1r4a.cif.gz | 191 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1r4a.ent.gz | 151.6 KB | Display | PDB format |
PDBx/mmJSON format | 1r4a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r4/1r4a ftp://data.pdbj.org/pub/pdb/validation_reports/r4/1r4a | HTTPS FTP |
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-Related structure data
Related structure data | 1ksgS S: Starting model for refinement |
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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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Details | Four molecules are generated by two 2-fold symmetry operations. / Tetramer is generated by two 2-fold symmetry operations. |
-Components
#1: Protein | Mass: 18737.615 Da / Num. of mol.: 4 / Fragment: Arl1 (Residue 16-180) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: ARL1 / Plasmid: pGEX-6p-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 star / References: UniProt: P61212 #2: Protein | Mass: 6198.274 Da / Num. of mol.: 4 / Fragment: GRIP Domain (Residue 2172-2222) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GOLGIN-245 / Plasmid: pGEX-6p-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 star / References: UniProt: Q13439 #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-GNP / #5: Water | ChemComp-HOH / | |
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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: 2.6 Å3/Da / Density % sol: 52.35 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: PEG3350, potassium thiocyanate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / 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: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.972 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 10, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.972 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→99.9 Å / Num. all: 55269 / Num. obs: 55268 / % possible obs: 91 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rmerge(I) obs: 0.075 / Rsym value: 0.075 / Net I/σ(I): 8.4 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.539 / Mean I/σ(I) obs: 1.88 / Rsym value: 0.479 / % possible all: 56.5 |
Reflection | *PLUS Lowest resolution: 39 Å / % possible obs: 97.1 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1KSG Resolution: 2.3→20 Å / Cross valid method: free R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: The structure was refined also with CNS(BRUNGER)
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Refinement step | Cycle: LAST / Resolution: 2.3→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.39 Å / Total num. of bins used: 20 /
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Software | *PLUS Version: 5 / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.26 / Rfactor Rwork: 0.245 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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