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- PDB-4nt2: Crystal structure of Arabidopsis ACD11 (accelerated-cell-death 11... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4nt2 | ||||||
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Title | Crystal structure of Arabidopsis ACD11 (accelerated-cell-death 11) complexed with lyso-sphingomyelin (d18:1) at 2.4 Angstrom resolution | ||||||
![]() | accelerated-cell-death 11 | ||||||
![]() | TRANSPORT PROTEIN / protein-lipid complexes / GLTP-fold / lipid transfer protein / cell death / LysoSM / lysosphingomyelin / ceramide-1-phosphate / C1P | ||||||
Function / homology | ![]() sphingomyelin transfer activity / response to salicylic acid / cell death / defense response to bacterium / lipid binding / cytoplasm 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 | ![]() | 100.2 KB | Display | ![]() |
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PDB format | ![]() | 76.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4nt1SC ![]() 4ntgC ![]() 4ntiC ![]() 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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1 |
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 22797.480 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||||
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#2: Chemical | #3: Chemical | ChemComp-SO4 / #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.94 Å3/Da / Density % sol: 68.76 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1 M Bis-Tris, pH 6.5, 2 M ammonium sulfate, 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: Apr 22, 2009 |
Radiation | Monochromator: Cryogenically-cooled single crystal Si(220) side bounce Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. obs: 14869 / % possible obs: 97.8 % / Redundancy: 7.4 % / Biso Wilson estimate: 41.62 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 24.5 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.451 / Mean I/σ(I) obs: 1.96 |
-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4NT1 Resolution: 2.403→35.622 Å / Occupancy max: 1 / Occupancy min: 0.44 / FOM work R set: 0.8254 / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 23.29 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 1 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 139.22 Å2 / Biso mean: 42.2653 Å2 / Biso min: 16.01 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.403→35.622 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: 5
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Refinement TLS params. | Method: refined / Origin x: -33.6985 Å / Origin y: -27.2843 Å / Origin z: 5.0594 Å
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Refinement TLS group | Selection details: all |