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Yorodumi- PDB-5zyk: Crystal structure of CERT START domain in complex with compound E25 -
+Open data
-Basic information
Entry | Database: PDB / ID: 5zyk | ||||||
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Title | Crystal structure of CERT START domain in complex with compound E25 | ||||||
Components | LIPID-TRANSFER PROTEIN CERT | ||||||
Keywords | LIPID TRANSPORT / CERT / PH / START / COMPLEX | ||||||
Function / homology | Function and homology information 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 / lipid homeostasis / endoplasmic reticulum organization / phosphatidylinositol-4-phosphate binding / 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.55 Å | ||||||
Authors | Suzuki, M. / Nakao, N. / Ueno, M. / Sakai, S. / Egawa, D. / Hanzawa, H. / Kawasaki, S. / Kumagai, K. / Kobayashi, S. / Hanada, K. | ||||||
Citation | Journal: Commun Chem / Year: 2019 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5zyk.cif.gz | 74.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5zyk.ent.gz | 52.7 KB | Display | PDB format |
PDBx/mmJSON format | 5zyk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5zyk_validation.pdf.gz | 772.4 KB | Display | wwPDB validaton report |
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Full document | 5zyk_full_validation.pdf.gz | 777.8 KB | Display | |
Data in XML | 5zyk_validation.xml.gz | 16.4 KB | Display | |
Data in CIF | 5zyk_validation.cif.gz | 25.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zy/5zyk ftp://data.pdbj.org/pub/pdb/validation_reports/zy/5zyk | HTTPS FTP |
-Related structure data
Related structure data | 5zygC 5zyhC 5zyiC 5zyjC 5zylC 5zymC 6iezC 6if0C 6j0oC 6j81C C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Homo sapiens (human) / Gene: CERT / Plasmid: pET28b-His-3C-CERT START / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9Y5P4 |
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#2: Chemical | ChemComp-9MC / |
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.06 % |
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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: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Aug 29, 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: 1.5→25 Å / Num. obs: 45749 / % possible obs: 99.3 % / Redundancy: 6.768 % / Biso Wilson estimate: 24.074 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.043 / Rrim(I) all: 0.046 / Χ2: 0.99 / Net I/σ(I): 26.69 / Num. measured all: 309636 / Scaling rejects: 33 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
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Refinement | Resolution: 1.55→25 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.368 / SU ML: 0.05 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.08 / ESU R Free: 0.081 / 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: 69.18 Å2 / Biso mean: 19.821 Å2 / Biso min: 7.73 Å2
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Refinement step | Cycle: final / Resolution: 1.55→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.55→1.604 Å / Rfactor Rfree error: 0 / Total num. of bins used: 15
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