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- PDB-3abh: Crystal structure of the EFC/F-BAR domain of human PACSIN2/Syndap... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3abh | ||||||
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Title | Crystal structure of the EFC/F-BAR domain of human PACSIN2/Syndapin II (2.0 A) | ||||||
![]() | Protein kinase C and casein kinase substrate in neurons protein 2 | ||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Shimada, A. / Shirouzu, M. / Hanawa-Suetsugu, K. / Terada, T. / Umehara, T. / Suetsugu, S. / Yamamoto, M. / Yokoyama, S. | ||||||
![]() | ![]() Title: Mapping of the basic amino-acid residues responsible for tubulation and cellular protrusion by the EFC/F-BAR domain of pacsin2/Syndapin II Authors: Shimada, A. / Takano, K. / Shirouzu, M. / Hanawa-Suetsugu, K. / Terada, T. / Toyooka, K. / Umehara, T. / Yamamoto, M. / Yokoyama, S. / Suetsugu, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 142.3 KB | Display | ![]() |
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PDB format | ![]() | 112.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related 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: 36970.117 Da / Num. of mol.: 2 / Fragment: EFC/F-BAR domain 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: 3.25 Å3/Da / Density % sol: 62.15 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 10% PEG 3350, 0.1M ammonium fluoride, 0.01M Tris-HCl, 0.075M NaCl, 0.001M DTT, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 20, 2009 / Details: mirrors |
Radiation | Monochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2→50 Å / Num. obs: 64396 / % possible obs: 95.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Biso Wilson estimate: 15.1 Å2 / Rsym value: 0.119 / Net I/σ(I): 12.4 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 4.9 / Num. unique all: 6306 / Rsym value: 0.367 / % possible all: 96 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: Structure of the EFC/F-BAR domain of human PACSIN2 (AMINO ACIDS 1-343) Resolution: 2→48.59 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 59998.12 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 66.3319 Å2 / ksol: 0.386818 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→48.59 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
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Xplor file |
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