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- PDB-5zyi: Crystal structure of CERT START domain in complex with compound E16 -
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Open data
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Basic information
Entry | Database: PDB / ID: 5zyi | ||||||
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Title | Crystal structure of CERT START domain in complex with compound E16 | ||||||
![]() | LIPID-TRANSFER PROTEIN CERT | ||||||
![]() | LIPID TRANSPORT / CERT / PH / START / COMPLEX | ||||||
Function / homology | ![]() intermembrane sphingolipid transfer / ceramide transfer activity / ER to Golgi ceramide transport / ceramide 1-phosphate binding / ceramide 1-phosphate transfer activity / ceramide transport / ceramide binding / ceramide metabolic process / intermembrane lipid transfer / Sphingolipid de novo biosynthesis ...intermembrane sphingolipid transfer / ceramide transfer activity / ER to Golgi ceramide transport / ceramide 1-phosphate binding / ceramide 1-phosphate transfer activity / ceramide transport / ceramide binding / ceramide metabolic process / intermembrane lipid transfer / Sphingolipid de novo biosynthesis / endoplasmic reticulum organization / phosphatidylinositol-4-phosphate binding / lipid homeostasis / heart morphogenesis / muscle contraction / response to endoplasmic reticulum stress / mitochondrion organization / cell morphogenesis / kinase activity / in utero embryonic development / cell population proliferation / immune response / endoplasmic reticulum membrane / Golgi apparatus / signal transduction / mitochondrion / nucleoplasm / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() | ||||||
![]() | Suzuki, M. / Nakao, N. / Ueno, M. / Sakai, S. / Egawa, D. / Hanzawa, H. / Kawasaki, S. / Kumagai, K. / Kobayashi, S. / Hanada, K. | ||||||
![]() | ![]() Title: Natural ligand-nonmimetic inhibitors of the lipid-transfer protein CERT Authors: Nakao, N. / Ueno, M. / Sakai, S. / Egawa, D. / Hanzawa, H. / Kawasaki, S. / Kumagai, K. / Suzuki, M. / Kobayashi, S. / Hanada, 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 | ![]() | 65.8 KB | Display | ![]() |
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PDB format | ![]() | 46.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5zygC ![]() 5zyhC ![]() 5zyjC ![]() 5zykC ![]() 5zylC ![]() 5zymC ![]() 6iezC ![]() 6if0C ![]() 6j0oC ![]() 6j81C 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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Unit cell |
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Components
#1: Protein | Mass: 27056.781 Da / Num. of mol.: 1 / Fragment: UNP residues 364-598 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-9ML / |
#3: Water | ChemComp-HOH / |
Sequence details | Two residues GLY362A and PRO363A are originated from protease site after N-terminal affinity tag. ...Two residues GLY362A and PRO363A are originated from protease site after N-terminal affinity tag. THIS SEQUENCE CORRESPOND |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 51.97 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.9 Details: 0.1M trisodium citrate/HCl buffer, pH 5.9, containing 24% PEG3350 and 0.2% n-octyl-beta-D-glucoside |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Jul 22, 2017 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.8→25 Å / Num. obs: 26872 / % possible obs: 99.5 % / Redundancy: 6.798 % / Biso Wilson estimate: 36.071 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.051 / Rrim(I) all: 0.055 / Χ2: 0.982 / Net I/σ(I): 21.01 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Resolution: 1.9→25 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.936 / SU B: 4.086 / SU ML: 0.117 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.158 / ESU R Free: 0.148 / Details: U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 104.23 Å2 / Biso mean: 32.443 Å2 / Biso min: 12.98 Å2
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Refinement step | Cycle: final / Resolution: 1.9→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.966 Å / Rfactor Rfree error: 0 / Total num. of bins used: 15
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