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Yorodumi- PDB-3sjh: Crystal Structure of a chimera containing the N-terminal domain (... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3sjh | ||||||
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Title | Crystal Structure of a chimera containing the N-terminal domain (residues 8-29) of drosophila Ciboulot and the C-terminal domain (residues 18-44) of bovine Thymosin-beta4, bound to G-actin-ATP-Latrunculin A | ||||||
Components |
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Keywords | CONTRACTILE PROTEIN / PROTEIN BINDING / protein-protein complex | ||||||
Function / homology | Function and homology information larval central nervous system remodeling / positive regulation of neutrophil migration / sequestering of actin monomers / negative regulation of neutrophil chemotaxis / cellular response to glucocorticoid stimulus / cytoskeletal motor activator activity / positive regulation of wound healing / tropomyosin binding / myosin heavy chain binding / mesenchyme migration ...larval central nervous system remodeling / positive regulation of neutrophil migration / sequestering of actin monomers / negative regulation of neutrophil chemotaxis / cellular response to glucocorticoid stimulus / cytoskeletal motor activator activity / positive regulation of wound healing / tropomyosin binding / myosin heavy chain binding / mesenchyme migration / troponin I binding / actin filament bundle / filamentous actin / actin filament bundle assembly / skeletal muscle thin filament assembly / striated muscle thin filament / skeletal muscle myofibril / actin monomer binding / skeletal muscle fiber development / stress fiber / regulation of cell migration / titin binding / actin filament polymerization / protein sequestering activity / filopodium / actin filament organization / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / brain development / negative regulation of inflammatory response / calcium-dependent protein binding / lamellipodium / cell body / cytoskeleton / hydrolase activity / protein domain specific binding / calcium ion binding / positive regulation of gene expression / magnesium ion binding / extracellular space / ATP binding / identical protein binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Drosophila melanogaster (fruit fly) Bos taurus (cattle) Oryctolagus cuniculus (rabbit) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å | ||||||
Authors | Renault, L. / Husson, C. / Carlier, M.F. / Didry, D. | ||||||
Citation | Journal: Embo J. / Year: 2012 Title: How a single residue in individual beta-thymosin/WH2 domains controls their functions in actin assembly Authors: Didry, D. / Cantrelle, F.X. / Husson, C. / Roblin, P. / Moorthy, A.M. / Perez, J. / Le Clainche, C. / Hertzog, M. / Guittet, E. / Carlier, M.F. / van Heijenoort, C. / Renault, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3sjh.cif.gz | 175.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3sjh.ent.gz | 135.5 KB | Display | PDB format |
PDBx/mmJSON format | 3sjh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sj/3sjh ftp://data.pdbj.org/pub/pdb/validation_reports/sj/3sjh | HTTPS FTP |
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-Related structure data
Related structure data | 3u8xC 3u9dC 3u9zC 1sqkS 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
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 41862.613 Da / Num. of mol.: 1 / Fragment: UNP residues 3-377 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Organ: alpha Skeletal Muscle / References: UniProt: P68135 |
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#2: Protein | Mass: 5988.682 Da / Num. of mol.: 1 Fragment: UNP O97428 residues 8-29, UNP P62326 residues 18-44 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly), (gene. exp.) Bos taurus (cattle) Gene: cib, EG:EG0007.11, CG4944, Dmel_CG4944 / Plasmid: pGEX-6P1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O97428, UniProt: P62326 |
-Non-polymers , 4 types, 362 molecules
#3: Chemical | ChemComp-ATP / |
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#4: Chemical | ChemComp-MG / |
#5: Chemical | ChemComp-LAR / |
#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: 2.28 Å3/Da / Density % sol: 46.08 % |
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Crystal grow | Temperature: 298 K / Method: hanging drop / pH: 6.5 Details: 22% PEG3350, 0.2M MgAcetate pH6.5, 0.45M Guanidine HCl, 1% Dioxane, hanging drop, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.98 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 21, 2006 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Highest resolution: 1.75 Å / Num. obs: 44860 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 24.372 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 26.62 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1SQK Resolution: 1.75→26.88 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.947 / WRfactor Rfree: 0.2092 / WRfactor Rwork: 0.1777 / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.8859 / SU B: 4.268 / SU ML: 0.063 / SU R Cruickshank DPI: 0.1055 / SU Rfree: 0.1023 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
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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: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 54.65 Å2 / Biso mean: 18.827 Å2 / Biso min: 2 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→26.88 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.751→1.796 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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