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Open data
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Basic information
Entry | Database: PDB / ID: 5a1k | ||||||
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Title | Crystal structure of calcium-free human adseverin domains A1-A3 | ||||||
![]() | ADSEVERIN | ||||||
![]() | ACTIN-BINDING PROTEIN / ACTIN | ||||||
Function / homology | ![]() positive regulation of secretion / regulation of chondrocyte differentiation / 1-phosphatidylinositol binding / actin nucleation / positive regulation of actin nucleation / positive regulation of megakaryocyte differentiation / sequestering of actin monomers / calcium-ion regulated exocytosis / actin filament severing / actin filament capping ...positive regulation of secretion / regulation of chondrocyte differentiation / 1-phosphatidylinositol binding / actin nucleation / positive regulation of actin nucleation / positive regulation of megakaryocyte differentiation / sequestering of actin monomers / calcium-ion regulated exocytosis / actin filament severing / actin filament capping / actin polymerization or depolymerization / barbed-end actin filament capping / cell projection assembly / podosome / anchoring junction / phosphatidylserine binding / brush border / phosphatidylinositol-4,5-bisphosphate binding / central nervous system development / cell projection / actin filament binding / actin cytoskeleton / actin binding / cell cortex / positive regulation of apoptotic process / negative regulation of cell population proliferation / calcium ion binding / extracellular exosome / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Chumnarnsilpa, S. / Robinson, R.C. / Grimes, J.M. / Leyrat, C. | ||||||
![]() | ![]() Title: Calcium-Controlled Conformational Choreography in the N-Terminal Half of Adseverin. Authors: Chumnarnsilpa, S. / Robinson, R.C. / Grimes, J.M. / Leyrat, C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 275.5 KB | Display | ![]() |
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PDB format | ![]() | 225.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5a1mC ![]() 1d0nS 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.551, 0.834), Vector: |
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Components
#1: Protein | Mass: 38799.824 Da / Num. of mol.: 2 / Fragment: DOMAINS A1-A3, RESIDUES 6-349 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 47.3 % / Description: NONE |
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Crystal grow | Details: 20 % POLYETHYLENE GLYCOL 3350, 100 MM BIS-TRIS PROPANE PH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 12, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0033 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→59.6 Å / Num. obs: 17766 / % possible obs: 98 % / Observed criterion σ(I): 1.5 / Redundancy: 5.5 % / Biso Wilson estimate: 79.21 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 5.5 % / Rmerge(I) obs: 1.33 / Mean I/σ(I) obs: 1.5 / % possible all: 95 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1D0N RESIDUES 27-370 Resolution: 2.9→59.63 Å / Cor.coef. Fo:Fc: 0.8906 / Cor.coef. Fo:Fc free: 0.8939 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.393 Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
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Displacement parameters | Biso mean: 55.6 Å2
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Refine analyze | Luzzati coordinate error obs: 0.499 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→59.63 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→3.08 Å / Total num. of bins used: 9
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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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