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- PDB-4nti: Crystal structure of D60N mutant of Arabidopsis ACD11 (accelerate... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4nti | ||||||
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Title | Crystal structure of D60N mutant of Arabidopsis ACD11 (accelerated-cell-death 11) complexed with C12 ceramide-1-phosphate (d18:1/12:0) at 2.9 Angstrom resolution | ||||||
![]() | accelerated-cell-death 11 | ||||||
![]() | TRANSPORT PROTEIN / protein-lipid complexes / GLTP-fold / lipid transfer protein / cell death / ceramide-1-phosphate / C1P | ||||||
Function / homology | ![]() sphingomyelin transfer activity / response to salicylic acid / ceramide 1-phosphate binding / ceramide 1-phosphate transfer activity / ER to Golgi ceramide transport / cell death / defense response to bacterium / membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Simanshu, D.K. / Brown, R.E. / Patel, D.J. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 175.4 KB | Display | ![]() |
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PDB format | ![]() | 140.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 18.4 KB | Display | |
Data in CIF | ![]() | 23.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4nt1SC ![]() 4nt2C ![]() 4ntgC ![]() 4ntoC 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 22796.496 Da / Num. of mol.: 2 / Mutation: D60N Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-1PZ / ( #3: Chemical | ChemComp-PEG / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 6.73 Å3/Da / Density % sol: 81.72 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.1 M MIB buffer, pH 8.0, 25% PEG1500, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 18, 2010 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: cryo-cooled double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.899→50 Å / Num. obs: 27802 / % possible obs: 99.9 % / Redundancy: 4.7 % / Biso Wilson estimate: 58.8 Å2 / Rmerge(I) obs: 0.094 / Χ2: 0.829 / Net I/σ(I): 6.5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4NT1 Resolution: 2.899→48.488 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8395 / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.77 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 181.78 Å2 / Biso mean: 47.7177 Å2 / Biso min: 12.44 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.899→48.488 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: -63.02 Å / Origin y: 24.0035 Å / Origin z: -13.4807 Å
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Refinement TLS group |
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