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Yorodumi- PDB-1rdw: Actin Crystal Dynamics: Structural Implications for F-actin Nucle... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1rdw | ||||||
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Title | Actin Crystal Dynamics: Structural Implications for F-actin Nucleation, Polymerization and Branching Mediated by the Anti-parallel Dimer | ||||||
Components | Actin, alpha skeletal muscle | ||||||
Keywords | STRUCTURAL PROTEIN / Anti-parallel dimer / Polymerization / Nucleation / Filament | ||||||
Function / homology | Function and homology information cytoskeletal motor activator activity / tropomyosin binding / mesenchyme migration / troponin I binding / myosin heavy chain binding / filamentous actin / actin filament bundle / skeletal muscle thin filament assembly / striated muscle thin filament / actin filament bundle assembly ...cytoskeletal motor activator activity / tropomyosin binding / mesenchyme migration / troponin I binding / myosin heavy chain binding / filamentous actin / actin filament bundle / skeletal muscle thin filament assembly / striated muscle thin filament / actin filament bundle assembly / skeletal muscle myofibril / actin monomer binding / skeletal muscle fiber development / stress fiber / titin binding / actin filament polymerization / filopodium / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / calcium-dependent protein binding / lamellipodium / cell body / hydrolase activity / protein domain specific binding / calcium ion binding / positive regulation of gene expression / magnesium ion binding / ATP binding / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | Oryctolagus cuniculus (rabbit) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Reutzel, R. / Yoshioka, C. / Govindasamy, L. / Yarmola, E.G. / Agbandje-Mckenna, M. / Bubb, M.R. / Mckenna, R. | ||||||
Citation | Journal: J.Struct.Biol. / Year: 2004 Title: Actin crystal dynamics: structural implications for F-actin nucleation, polymerization, and branching mediated by the anti-parallel dimer. Authors: Reutzel, R. / Yoshioka, C. / Govindasamy, L. / Yarmola, E.G. / Agbandje-McKenna, M. / Bubb, M.R. / McKenna, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1rdw.cif.gz | 90.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rdw.ent.gz | 67.3 KB | Display | PDB format |
PDBx/mmJSON format | 1rdw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1rdw_validation.pdf.gz | 537.5 KB | Display | wwPDB validaton report |
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Full document | 1rdw_full_validation.pdf.gz | 550.9 KB | Display | |
Data in XML | 1rdw_validation.xml.gz | 11.4 KB | Display | |
Data in CIF | 1rdw_validation.cif.gz | 16.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rd/1rdw ftp://data.pdbj.org/pub/pdb/validation_reports/rd/1rdw | HTTPS FTP |
-Related structure data
Related structure data | 1rfqC 1lcuS 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: 41862.613 Da / Num. of mol.: 1 / Fragment: ACtin Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Tissue: muscle / Gene: ACTA1, ACTA / References: UniProt: P68135 | ||||||
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#2: Chemical | #3: Chemical | ChemComp-ATP / | #4: Chemical | ChemComp-LAR / | #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: 3.16 Å3/Da / Density % sol: 61.04 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 6.7 Details: MgCl2, NH4SO4, pH 6.7, VAPOR DIFFUSION, HANGING DROP | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion / Details: Bubb, M.R., (2002) J. Biol. Chem., 277, 20999. | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 273 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Details: Osmic mirrors |
Radiation | Monochromator: CuKalpha / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→20 Å / Num. obs: 22951 / % possible obs: 93.9 % / Rsym value: 0.093 |
Reflection shell | Resolution: 2.3→2.38 Å / Num. unique all: 22951 / Rsym value: 0.424 / % possible all: 92.1 |
Reflection | *PLUS Rmerge(I) obs: 0.093 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1LCU Resolution: 2.3→20 Å / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 38.346 Å2 | ||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→20 Å
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Refine LS restraints |
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Software | *PLUS Version: 5 / Classification: refinement | ||||||||||||||||
Refinement | *PLUS % reflection Rfree: 5 % | ||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||
Refine LS restraints | *PLUS
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