+Open data
-Basic information
Entry | Database: PDB / ID: 3dof | ||||||
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Title | Complex of ARL2 and BART, Crystal Form 2 | ||||||
Components |
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Keywords | SIGNALING PROTEIN/HYDROLASE / ADP-ribosylation factor-like 2 / binder of ARL2 / small GTPase / effector / complex structure / GTP-binding / Lipoprotein / Myristate / Nucleotide-binding / Polymorphism / Alternative splicing / Cytoplasm / Mitochondrion / Phosphoprotein / SIGNALING PROTEIN-HYDROLASE COMPLEX | ||||||
Function / homology | Function and homology information Transport of nucleosides and free purine and pyrimidine bases across the plasma membrane / GTPase regulator activity / Post-chaperonin tubulin folding pathway / bicellular tight junction assembly / maintenance of protein location in nucleus / centrosome cycle / positive regulation of cell-substrate adhesion / regulation of glycolytic process / negative regulation of GTPase activity / regulation of aerobic respiration ...Transport of nucleosides and free purine and pyrimidine bases across the plasma membrane / GTPase regulator activity / Post-chaperonin tubulin folding pathway / bicellular tight junction assembly / maintenance of protein location in nucleus / centrosome cycle / positive regulation of cell-substrate adhesion / regulation of glycolytic process / negative regulation of GTPase activity / regulation of aerobic respiration / regulation of microtubule polymerization / lateral plasma membrane / positive regulation of tyrosine phosphorylation of STAT protein / positive regulation of microtubule polymerization / mitochondrial intermembrane space / cilium / spindle / RAS processing / GDP binding / microtubule cytoskeleton / protein folding / midbody / transcription coactivator activity / mitochondrial matrix / focal adhesion / GTPase activity / centrosome / GTP binding / nucleolus / Golgi apparatus / signal transduction / mitochondrion / nucleoplasm / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å | ||||||
Authors | Zhang, T. / Li, S. / Ding, J. | ||||||
Citation | Journal: Structure / Year: 2009 Title: Crystal structure of the ARL2-GTP-BART complex reveals a novel recognition and binding mode of small GTPase with effector Authors: Zhang, T. / Li, S. / Zhang, Y. / Zhong, C. / Lai, Z. / Ding, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3dof.cif.gz | 132.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3dof.ent.gz | 101.2 KB | Display | PDB format |
PDBx/mmJSON format | 3dof.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3dof_validation.pdf.gz | 738 KB | Display | wwPDB validaton report |
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Full document | 3dof_full_validation.pdf.gz | 744.2 KB | Display | |
Data in XML | 3dof_validation.xml.gz | 14.2 KB | Display | |
Data in CIF | 3dof_validation.cif.gz | 18.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/do/3dof ftp://data.pdbj.org/pub/pdb/validation_reports/do/3dof | HTTPS FTP |
-Related structure data
Related structure data | 3doeC 1ksgS C: citing same article (ref.) 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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-Components
#1: Protein | Mass: 21975.146 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): DE3 / References: UniProt: P36404 |
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#2: Protein | Mass: 18981.176 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX-4T-1 / Production host: Escherichia coli (E. coli) / Strain (production host): DE3 / References: UniProt: Q9Y2Y0 |
#3: Chemical | ChemComp-GTP / |
#4: Chemical | ChemComp-MG / |
#5: 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: 2.17 Å3/Da / Density % sol: 43.2 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.9 Details: 0.2M MgCl2, 20% PEG 3350, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 4, 2007 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→50 Å / Num. all: 5853 / Num. obs: 5818 / % possible obs: 99.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.3 % / Biso Wilson estimate: 87.4 Å2 / Rmerge(I) obs: 0.161 / Rsym value: 0.161 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 3.3→3.42 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.759 / Mean I/σ(I) obs: 2.4 / Num. unique all: 565 / Rsym value: 0.759 / % possible all: 97.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1KSG Resolution: 3.3→40.18 Å / Cor.coef. Fo:Fc: 0.904 / Cor.coef. Fo:Fc free: 0.874 / SU B: 77.253 / SU ML: 0.539 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.676 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 76.322 Å2
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Refinement step | Cycle: LAST / Resolution: 3.3→40.18 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.3→3.385 Å / Total num. of bins used: 20
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