+Open data
-Basic information
Entry | Database: PDB / ID: 4edm | ||||||
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Title | Crystal structure of beta-parvin CH2 domain | ||||||
Components | Beta-parvin | ||||||
Keywords | SIGNALING PROTEIN / calponin homology domain / protein-protein interaction / LD motif / integrin signaling / focal adhesion / Adaptor protein / Paxillin / Integrin linked kinase | ||||||
Function / homology | Function and homology information establishment or maintenance of cell polarity regulating cell shape / Regulation of cytoskeletal remodeling and cell spreading by IPP complex components / Cell-extracellular matrix interactions / cell projection assembly / lamellipodium assembly / establishment or maintenance of cell polarity / substrate adhesion-dependent cell spreading / Z disc / actin cytoskeleton / lamellipodium ...establishment or maintenance of cell polarity regulating cell shape / Regulation of cytoskeletal remodeling and cell spreading by IPP complex components / Cell-extracellular matrix interactions / cell projection assembly / lamellipodium assembly / establishment or maintenance of cell polarity / substrate adhesion-dependent cell spreading / Z disc / actin cytoskeleton / lamellipodium / actin binding / actin cytoskeleton organization / focal adhesion / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Stiegler, A.L. / Draheim, K.M. / Li, X. / Chayen, N.E. / Calderwood, D.A. / Boggon, T.J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2012 Title: Structural basis for paxillin binding and focal adhesion targeting of beta-parvin. Authors: Stiegler, A.L. / Draheim, K.M. / Li, X. / Chayen, N.E. / Calderwood, D.A. / Boggon, T.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4edm.cif.gz | 120.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4edm.ent.gz | 97.2 KB | Display | PDB format |
PDBx/mmJSON format | 4edm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ed/4edm ftp://data.pdbj.org/pub/pdb/validation_reports/ed/4edm | HTTPS FTP |
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-Related 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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-Components
#1: Protein | Mass: 15371.638 Da / Num. of mol.: 2 / Fragment: C-terminal calponin homology domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PARVB, CGI-56 / Plasmid: pCDFDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9HBI1 #2: Chemical | ChemComp-EDO / #3: 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: 2.86 Å3/Da / Density % sol: 57.02 % |
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Crystal grow | Temperature: 298 K / Method: microbatch / pH: 7.5 Details: 12% PEG 550 MME, 0.1M Tris, pH 7.5, Microbatch, temperature 298K |
-Data collection
Diffraction | Mean temperature: 173 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1.0781 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jul 2, 2010 / Details: mirror |
Radiation | Monochromator: Si(111) channel cut monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0781 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 23924 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.8 % / Biso Wilson estimate: 40.1 Å2 / Rsym value: 0.082 / Net I/σ(I): 25.891 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 1.905 / % possible all: 92.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.943 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 11.627 / SU ML: 0.154 / Cross valid method: THROUGHOUT / ESU R: 0.177 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 129.56 Å2 / Biso mean: 58.1985 Å2 / Biso min: 25.27 Å2
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Refinement step | Cycle: LAST / Resolution: 2→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.054 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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