+Open data
-Basic information
Entry | Database: PDB / ID: 1ksh | ||||||
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Title | Complex of Arl2 and PDE delta, Crystal Form 2 (native) | ||||||
Components |
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Keywords | SIGNALING PROTEIN/HYDROLASE / small GTPase / small GTP-binding protein / Arf family / effector molecule / immunoglobuline-like fold / GDI / SIGNALING PROTEIN-HYDROLASE COMPLEX | ||||||
Function / homology | Function and homology information Transport of nucleosides and free purine and pyrimidine bases across the plasma membrane / acetylcholine transport / ARL13B-mediated ciliary trafficking of INPP5E / RAS processing / GTPase inhibitor activity / bicellular tight junction assembly / maintenance of protein location in nucleus / centrosome cycle / negative regulation of GTPase activity / positive regulation of cell-substrate adhesion ...Transport of nucleosides and free purine and pyrimidine bases across the plasma membrane / acetylcholine transport / ARL13B-mediated ciliary trafficking of INPP5E / RAS processing / GTPase inhibitor activity / bicellular tight junction assembly / maintenance of protein location in nucleus / centrosome cycle / negative regulation of GTPase activity / positive regulation of cell-substrate adhesion / regulation of glycolytic process / regulation of aerobic respiration / regulation of microtubule polymerization / lateral plasma membrane / positive regulation of microtubule polymerization / visual perception / cytoplasmic vesicle membrane / cilium / mitochondrial intermembrane space / small GTPase binding / RAS processing / GDP binding / microtubule cytoskeleton / protein folding / cytoplasmic vesicle / cytoskeleton / focal adhesion / GTPase activity / centrosome / GTP binding / nucleolus / Golgi apparatus / mitochondrion / nucleoplasm / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / combination of Molecular Replacement, SAD phasing / Resolution: 1.8 Å | ||||||
Authors | Hanzal-Bayer, M. / Renault, L. / Roversi, P. / Wittinghofer, A. / Hillig, R.C. | ||||||
Citation | Journal: EMBO J. / Year: 2002 Title: The complex of Arl2-GTP and PDE delta: from structure to function. Authors: Hanzal-Bayer, M. / Renault, L. / Roversi, P. / Wittinghofer, A. / Hillig, R.C. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2001 Title: Coexpression, copurification, crystallization and preliminary X-ray analysis of a complex of Arl2-GTP and PDE delta Authors: Renault, L. / Hanzal-Bayer, M. / Hillig, R.C. #2: Journal: Structure / Year: 2000 Title: Structural and biochemical properties show Arl3-GDP as a distinct GTP-binding protein Authors: Hillig, R.C. / Hanzal-Bayer, M. / Linari, M. / Becker, J. / Wittinghofer, A. / Renault, L. #3: Journal: FEBS Lett. / Year: 1999 Title: The delta subunit of rod specific cyclic GMP phosphodiesterase, PDE delta, interacts with the Arf-like protein Arl3 in a GTP specific manner Authors: Linari, M. / Hanzal-Bayer, M. / Becker, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ksh.cif.gz | 83.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ksh.ent.gz | 61.3 KB | Display | PDB format |
PDBx/mmJSON format | 1ksh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ksh_validation.pdf.gz | 821.2 KB | Display | wwPDB validaton report |
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Full document | 1ksh_full_validation.pdf.gz | 828.8 KB | Display | |
Data in XML | 1ksh_validation.xml.gz | 16.6 KB | Display | |
Data in CIF | 1ksh_validation.cif.gz | 22.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ks/1ksh ftp://data.pdbj.org/pub/pdb/validation_reports/ks/1ksh | HTTPS FTP |
-Related structure data
Related structure data | 1ksgC 1ksjC 1fzqS 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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Details | The deposited coordinates represent the biological assembly (consisting of one Arl2 molecule (bound to GDP/PO4) and one PDE delta molecule). |
-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 21110.170 Da / Num. of mol.: 1 / Mutation: S33L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: ARL2 / Plasmid: pGEX KG / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: Q9D0J4 |
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#2: Protein | Mass: 17661.240 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PDE6D or PDED / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): B834 References: UniProt: O43924, 3',5'-cyclic-nucleotide phosphodiesterase |
-Non-polymers , 4 types, 127 molecules
#3: Chemical | ChemComp-MG / |
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#4: Chemical | ChemComp-PO4 / |
#5: Chemical | ChemComp-GDP / |
#6: 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: 1.9 Å3/Da / Density % sol: 36.2 % | ||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG 5000 MME, HEPES, MgCl2, beta mercaptoethanol, GTP, glycerol/xylitol as cryo protectant, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||
Crystal grow | *PLUS Details: Renault, L., (2001) Acta Crystallogr., Sect.D, 57, 1167. | ||||||||||||||||||
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: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.005 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 23, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.005 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→34.7 Å / Num. all: 28815 / Num. obs: 28815 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.6 % / Biso Wilson estimate: 19.8 Å2 / Rsym value: 0.042 / Net I/σ(I): 38.8 |
Reflection shell | Resolution: 1.8→1.84 Å / Redundancy: 7.9 % / Mean I/σ(I) obs: 4.8 / Rsym value: 0.316 / % possible all: 98.9 |
Reflection | *PLUS Highest resolution: 1.8 Å / Rmerge(I) obs: 0.042 |
Reflection shell | *PLUS % possible obs: 98.9 % / Rmerge(I) obs: 0.316 |
-Processing
Software |
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Refinement | Method to determine structure: combination of Molecular Replacement, SAD phasing Starting model: ARL3-GDP, pdb entry 1fzq Resolution: 1.8→34.68 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1490569.83 / Data cutoff low absF: 0 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 43.4906 Å2 / ksol: 0.315861 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 40 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→34.68 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Lowest resolution: 34.7 Å / % reflection Rfree: 10 % / Rfactor all: 0.247 / Rfactor obs: 0.244 / Rfactor Rfree: 0.271 / Rfactor Rwork: 0.244 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.45 / Rfactor Rwork: 0.413 / Rfactor obs: 0.413 |