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Yorodumi- PDB-4nto: Crystal structure of D60A mutant of Arabidopsis ACD11 (accelerate... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4nto | ||||||
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Title | Crystal structure of D60A mutant of Arabidopsis ACD11 (accelerated-cell-death 11) complexed with C2 ceramide-1-phosphate (d18:1/2:0) at 2.15 Angstrom resolution | ||||||
Components | accelerated-cell-death 11 | ||||||
Keywords | TRANSPORT PROTEIN / protein-lipid complexes / pi-bulge / GLTP-fold / lipid transfer protein / cell death / ceramide-1-phosphate / C1P | ||||||
Function / homology | Function and homology information sphingomyelin transfer activity / response to salicylic acid / cell death / defense response to bacterium / lipid binding / cytoplasm Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.152 Å | ||||||
Authors | Simanshu, D.K. / Brown, R.E. / Patel, D.J. | ||||||
Citation | Journal: Cell Rep / Year: 2014 Title: Arabidopsis Accelerated Cell Death 11, ACD11, Is a Ceramide-1-Phosphate Transfer Protein and Intermediary Regulator of Phytoceramide Levels. Authors: Simanshu, D.K. / Zhai, X. / Munch, D. / Hofius, D. / Markham, J.E. / Bielawski, J. / Bielawska, A. / Malinina, L. / Molotkovsky, J.G. / Mundy, J.W. / Patel, D.J. / Brown, R.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4nto.cif.gz | 258.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4nto.ent.gz | 211.7 KB | Display | PDB format |
PDBx/mmJSON format | 4nto.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nt/4nto ftp://data.pdbj.org/pub/pdb/validation_reports/nt/4nto | HTTPS FTP |
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-Related structure data
Related structure data | 4nt1SC 4nt2C 4ntgC 4ntiC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 22753.471 Da / Num. of mol.: 3 / Mutation: D60A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: ACD11, AT2G34690 / Plasmid: pET-SUMO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O64587 #2: Chemical | ChemComp-1PW / ( #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.88 Å3/Da / Density % sol: 57.27 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2 M sodium malonate, 0.1 M Bis-Tris propane, pH 6.5, 20% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97949 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 15, 2010 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: cryo-cooled double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.15→50 Å / Num. obs: 42665 / % possible obs: 99.3 % / Redundancy: 4.3 % / Biso Wilson estimate: 39.09 Å2 / Rmerge(I) obs: 0.074 / Χ2: 1.562 / Net I/σ(I): 9.5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4NT1 Resolution: 2.152→35.411 Å / Occupancy max: 1 / Occupancy min: 0.48 / FOM work R set: 0.8101 / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.81 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 126.98 Å2 / Biso mean: 41.5039 Å2 / Biso min: 16.97 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.152→35.411 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
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Refinement TLS params. | Method: refined / Origin x: -28.8167 Å / Origin y: -6.2889 Å / Origin z: 41.2296 Å
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Refinement TLS group |
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