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- PDB-2vzc: Crystal structure of the C-terminal calponin homology domain of a... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2vzc | ||||||
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Title | Crystal structure of the C-terminal calponin homology domain of alpha parvin | ||||||
![]() | ALPHA-PARVIN | ||||||
![]() | CELL ADHESION / MEMBRANE / CYTOPLASM / CYTOSKELETON / CELL JUNCTION / ALTERNATIVE SPLICING / CALPONIN HOMOLOGY DOMAIN / ACTIN-BINDING / CELL MEMBRANE | ||||||
Function / homology | ![]() actin-mediated cell contraction / smooth muscle cell chemotaxis / Regulation of cytoskeletal remodeling and cell spreading by IPP complex components / Localization of the PINCH-ILK-PARVIN complex to focal adhesions / Cell-extracellular matrix interactions / outflow tract septum morphogenesis / heterotypic cell-cell adhesion / sprouting angiogenesis / establishment or maintenance of cell polarity / protein kinase inhibitor activity ...actin-mediated cell contraction / smooth muscle cell chemotaxis / Regulation of cytoskeletal remodeling and cell spreading by IPP complex components / Localization of the PINCH-ILK-PARVIN complex to focal adhesions / Cell-extracellular matrix interactions / outflow tract septum morphogenesis / heterotypic cell-cell adhesion / sprouting angiogenesis / establishment or maintenance of cell polarity / protein kinase inhibitor activity / cilium assembly / substrate adhesion-dependent cell spreading / Z disc / actin cytoskeleton / lamellipodium / actin binding / regulation of cell shape / actin cytoskeleton organization / protein stabilization / cadherin binding / focal adhesion / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lorenz, S. / Vakonakis, I. / Lowe, E.D. / Campbell, I.D. / Noble, M.E.M. / Hoellerer, M.K. | ||||||
![]() | ![]() Title: Structural Analysis of the Interactions between Paxillin Ld Motifs and Alpha-Parvin Authors: Lorenz, S. / Vakonakis, I. / Lowe, E.D. / Campbell, I.D. / Noble, M.E.M. / Hoellerer, M.K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 154.4 KB | Display | ![]() |
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PDB format | ![]() | 125 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 488.8 KB | Display | ![]() |
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Full document | ![]() | 494.7 KB | Display | |
Data in XML | ![]() | 16.5 KB | Display | |
Data in CIF | ![]() | 24.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2vzdC ![]() 2vzgC ![]() 2vziC ![]() 1mb8S ![]() 1tjtS ![]() 1wkuS ![]() 2eyiS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 15155.380 Da / Num. of mol.: 2 Fragment: C-TERMINAL CALPONIN HOMOLOGY DOMAIN, RESIDUES 242-372 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 283 molecules ![](data/chem/img/TRS.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/MRD.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/MRD.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-TRS / |
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#3: Chemical | ChemComp-GOL / |
#4: Chemical | ChemComp-MRD / ( |
#5: Chemical | ChemComp-MPD / ( |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.36 % Description: MOLECULAR REPLACEMENT WITH ENSEMBLE OF CH1 DOMAINS FROM PDB ENTRIES 1WKU, 1TJT, 2EYI AND 1MB8 |
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Crystal grow | pH: 7.5 Details: 12% (W/V) PEG 8000, 35% (V/V) MPD, 0.1M HEPES PH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Nov 16, 2006 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.05→23.74 Å / Num. obs: 124910 / % possible obs: 93.7 % / Observed criterion σ(I): 2 / Redundancy: 4.2 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 16.5 |
Reflection shell | Resolution: 1.05→1.11 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.4 / % possible all: 77.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRIES 1WKU, 1TJT, 2EYI, 1MB8 Resolution: 1.05→46.42 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.97 / SU B: 0.805 / SU ML: 0.018 / Cross valid method: THROUGHOUT / ESU R: 0.029 / ESU R Free: 0.028 / 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: 9.28 Å2
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Refinement step | Cycle: LAST / Resolution: 1.05→46.42 Å
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