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- PDB-6ecm: Crystal Structure of SNX15 PX domain in domain swapped conformation -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ecm | ||||||||||||
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Title | Crystal Structure of SNX15 PX domain in domain swapped conformation | ||||||||||||
![]() | Sorting nexin-15![]() | ||||||||||||
![]() | LIPID BINDING PROTEIN / ![]() ![]() ![]() | ||||||||||||
Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Chandra, M. / Collins, B.M. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Classification of the human phox homology (PX) domains based on their phosphoinositide binding specificities. Authors: Chandra, M. / Chin, Y.K. / Mas, C. / Feathers, J.R. / Paul, B. / Datta, S. / Chen, K.E. / Jia, X. / Yang, Z. / Norwood, S.J. / Mohanty, B. / Bugarcic, A. / Teasdale, R.D. / Henne, W.M. / ...Authors: Chandra, M. / Chin, Y.K. / Mas, C. / Feathers, J.R. / Paul, B. / Datta, S. / Chen, K.E. / Jia, X. / Yang, Z. / Norwood, S.J. / Mohanty, B. / Bugarcic, A. / Teasdale, R.D. / Henne, W.M. / Mobli, M. / Collins, B.M. | ||||||||||||
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 | ![]() | 22.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5woeC ![]() 6edxC ![]() 6ee0C ![]() 6mbiC ![]() 4ikdS 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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Unit cell |
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Components
#1: Protein | ![]() Mass: 15134.136 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-SO4 / ![]() |
#3: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 40.01 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1 M Tris (pH 8.5) 200 mM LiSO4, 24% PEG4000, 10% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 1, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.35→45 Å / Num. obs: 5645 / % possible obs: 99.4 % / Redundancy: 26.2 % / CC1/2: 1 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.015 / Net I/σ(I): 20.9 |
Reflection shell | Resolution: 2.35→2.43 Å / Redundancy: 24.6 % / Rmerge(I) obs: 1.074 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 505 / CC1/2: 0.982 / Rpim(I) all: 0.216 / % possible all: 94.3 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 4IKD Resolution: 2.353→45 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 38.43
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.353→45 Å
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Refine LS restraints |
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LS refinement shell |
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