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- PDB-5nl7: The crystal structure of the Actin Binding Domain (ABD) of alpha ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5nl7 | ||||||
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Title | The crystal structure of the Actin Binding Domain (ABD) of alpha actinin from Entamoeba histolytica | ||||||
![]() | Calponin homology domain protein putative | ||||||
![]() | STRUCTURAL PROTEIN / Actin Binding Domain / Actinin / Entamoeba histolytica | ||||||
Function / homology | ![]() actin lateral binding / actomyosin contractile ring / actin filament bundle / actin filament bundle assembly / cell projection / cell junction / calcium ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pinotsis, N. / Djinovic-Carugo, K. / Khan, M.B. | ||||||
![]() | ![]() Title: Calcium modulates the domain flexibility and function of an alpha-actinin similar to the ancestral alpha-actinin. Authors: Pinotsis, N. / Zielinska, K. / Babuta, M. / Arolas, J.L. / Kostan, J. / Khan, M.B. / Schreiner, C. / Salmazo, A. / Ciccarelli, L. / Puchinger, M. / Gkougkoulia, E.A. / Ribeiro Jr., E.A. / ...Authors: Pinotsis, N. / Zielinska, K. / Babuta, M. / Arolas, J.L. / Kostan, J. / Khan, M.B. / Schreiner, C. / Salmazo, A. / Ciccarelli, L. / Puchinger, M. / Gkougkoulia, E.A. / Ribeiro Jr., E.A. / Marlovits, T.C. / Bhattacharya, A. / Djinovic-Carugo, 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 | ![]() | 199 KB | Display | ![]() |
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PDB format | ![]() | 160.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 453 KB | Display | ![]() |
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Full document | ![]() | 458.7 KB | Display | |
Data in XML | ![]() | 19.1 KB | Display | |
Data in CIF | ![]() | 26.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5nl6C ![]() 6sl2C ![]() 6sl3C ![]() 6sl7C ![]() 1wkuS S: Starting model for refinement C: citing same article ( |
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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 on special symmetry positions |
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Components
#1: Protein | Mass: 26432.672 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-CA / | #3: Chemical | ChemComp-TRS / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4 Å3/Da / Density % sol: 69.29 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.2 M Ca(CH3COO)2, 0.1 M Sodium Cacodylate pH 6.5 and 40% v/v PEG600 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Jun 6, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8426 Å / Relative weight: 1 |
Reflection | Resolution: 2.48→48.032 Å / Num. obs: 27759 / % possible obs: 95.6 % / Redundancy: 3.1 % / CC1/2: 0.995 / Rmerge(I) obs: 0.101 / Net I/av σ(I): 8.33 / Net I/σ(I): 8.33 |
Reflection shell | Resolution: 2.48→2.54 Å / Rmerge(I) obs: 0.647 / Mean I/σ(I) obs: 2.03 / Num. unique obs: 1951 / CC1/2: 0.398 / % possible all: 90.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1WKU Resolution: 2.48→48.032 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 2.02 / Phase error: 26.7 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.48→48.032 Å
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Refine LS restraints |
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LS refinement shell |
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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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