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Open data
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Basic information
Entry | Database: PDB / ID: 1svy | ||||||
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Title | SEVERIN DOMAIN 2, 1.75 ANGSTROM CRYSTAL STRUCTURE | ||||||
![]() | SEVERIN | ||||||
![]() | ACTIN-BINDING PROTEIN / CALCIUM-BINDING / CYTOSKELETON / GELSOLIN / SEVERIN / VILLIN / CALCIUM / PIP2 | ||||||
Function / homology | ![]() actin filament severing activity / actin filament fragmentation / Neutrophil degranulation / actin filament severing / barbed-end actin filament capping / actin polymerization or depolymerization / actin filament bundle assembly / actin monomer binding / phosphatidylinositol-4,5-bisphosphate binding / phagocytic vesicle ...actin filament severing activity / actin filament fragmentation / Neutrophil degranulation / actin filament severing / barbed-end actin filament capping / actin polymerization or depolymerization / actin filament bundle assembly / actin monomer binding / phosphatidylinositol-4,5-bisphosphate binding / phagocytic vesicle / calcium-dependent protein binding / actin filament binding / actin cytoskeleton / calcium ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Puius, Y.A. / Fedorov, E.V. / Eichinger, L. / Sullivan, M. / Schleicher, M. / Almo, S.C. | ||||||
![]() | ![]() Title: Mapping the functional surface of domain 2 in the gelsolin superfamily. Authors: Puius, Y.A. / Fedorov, E.V. / Eichinger, L. / Schleicher, M. / Almo, S.C. #1: ![]() Title: Structure of Severin Domain 2 in Solution Authors: Schnuchel, A. / Wiltscheck, R. / Eichinger, L. / Schleicher, M. / Holak, T.A. #2: ![]() Title: Characterization of Actin-and Lipid-Binding Domains in Severin, a Ca(2+)-Dependent F-Actin Fragmenting Protein Authors: Eichinger, L. / Schleicher, M. #3: ![]() Title: Severin, Gelsolin, and Villin Share a Homologous Sequence in Regions Presumed to Contain F-Actin Severing Domains Authors: Andre, E. / Lottspeich, F. / Schleicher, M. / Noegel, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 35.9 KB | Display | ![]() |
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PDB format | ![]() | 23.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 357.2 KB | Display | ![]() |
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Full document | ![]() | 357.2 KB | Display | |
Data in XML | ![]() | 3.3 KB | Display | |
Data in CIF | ![]() | 5.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 12276.842 Da / Num. of mol.: 1 / Fragment: DOMAIN 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-CA / |
#3: Chemical | ChemComp-NA / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 42 % | ||||||||||||||||||||
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Crystal grow | pH: 8 / Details: pH 8.0 | ||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 140 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: FUJI / Detector: IMAGE PLATE / Date: Feb 1, 1996 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→20 Å / Num. obs: 10235 / % possible obs: 93.1 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.035 / Net I/σ(I): 30.9 |
Reflection shell | Resolution: 1.75→1.81 Å / Rmerge(I) obs: 0.116 / Mean I/σ(I) obs: 9.9 / % possible all: 77.1 |
Reflection shell | *PLUS % possible obs: 77.1 % |
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Processing
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Refinement | Method to determine structure: ![]()
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Displacement parameters | Biso mean: 20.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.81 Å / Total num. of bins used: 10
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.2462 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor obs: 0.274 |