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Yorodumi- PDB-2q31: Actin Dimer Cross-linked Between Residues 41 and 374 and proteoly... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2q31 | ||||||
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Title | Actin Dimer Cross-linked Between Residues 41 and 374 and proteolytically cleaved by subtilisin between residues 47 and 48. | ||||||
Components | Actin, alpha skeletal muscle | ||||||
Keywords | STRUCTURAL PROTEIN / cross-linked dimer / proteolytically cleaved | ||||||
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 / SYNCHROTRON / difference Fourier / Resolution: 2.7 Å | ||||||
Authors | Sawaya, M.R. / Pashkov, I. / Kudryashov, D.S. / Reisler, E. / Yeates, T.O. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2008 Title: Multiple crystal structures of actin dimers and their implications for interactions in the actin filament. Authors: Sawaya, M.R. / Kudryashov, D.S. / Pashkov, I. / Adisetiyo, H. / Reisler, E. / Yeates, T.O. #1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2005 Title: The crystal structure of a cross-linked actin dimer suggests a detailed molecular interface in F-actin. Authors: Kudryashov, D.S. / Sawaya, M.R. / Adisetiyo, H. / Norcross, T. / Hegyi, G. / Reisler, E. / Yeates, T.O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2q31.cif.gz | 143.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2q31.ent.gz | 111.3 KB | Display | PDB format |
PDBx/mmJSON format | 2q31.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q3/2q31 ftp://data.pdbj.org/pub/pdb/validation_reports/q3/2q31 | HTTPS FTP |
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-Related structure data
Related structure data | 2q1nSC 2q36C 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: LAR / End label comp-ID: LAR / Refine code: 1 / Auth seq-ID: 5 - 402 / Label seq-ID: 5
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Details | Biological unit 1 is generated by a unit cell translation along the "c" axis applied to chain A. Biological unit 2 is generated by a unit cell translation along the "c" axis applied to chain B. |
-Components
#1: Protein | Mass: 41862.613 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P68135 #2: Chemical | #3: Chemical | #4: Chemical | #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: 2.46 Å3/Da / Density % sol: 50.03 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 30% MPD, 0.1 M sodium acetate, 0.01M calcium chloride, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 21, 2005 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double Crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.7→90 Å / Num. all: 19970 / Num. obs: 19970 / % possible obs: 87.5 % / Observed criterion σ(I): -3 / Redundancy: 2.8 % / Biso Wilson estimate: 47 Å2 / Rmerge(I) obs: 0.176 / Χ2: 1.042 / Net I/σ(I): 5.7 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: difference Fourier Starting model: pdb entry 2Q1N Resolution: 2.7→43.07 Å / Cor.coef. Fo:Fc: 0.874 / Cor.coef. Fo:Fc free: 0.826 / SU B: 33.536 / SU ML: 0.415 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 3 / ESU R Free: 0.547 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 24.744 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→43.07 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 4512 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.7→2.846 Å / Total num. of bins used: 10
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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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