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Yorodumi- PDB-4nt1: Crystal structure of apo-form of Arabidopsis ACD11 (accelerated-c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4nt1 | ||||||
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Title | Crystal structure of apo-form of Arabidopsis ACD11 (accelerated-cell-death 11) at 1.8 Angstrom resolution | ||||||
Components | accelerated-cell-death 11 | ||||||
Keywords | TRANSPORT PROTEIN / protein-lipid complexes / GLTP-fold / lipid transfer protein / cell death / ceramide-1-phosphate / C1P / lysine carboxylation | ||||||
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 / SIRAS / Resolution: 1.8 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 | 4nt1.cif.gz | 175 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4nt1.ent.gz | 145.7 KB | Display | PDB format |
PDBx/mmJSON format | 4nt1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nt/4nt1 ftp://data.pdbj.org/pub/pdb/validation_reports/nt/4nt1 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 22840.484 Da / Num. of mol.: 4 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-NA / | #3: 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: 2.31 Å3/Da / Density % sol: 46.68 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1 M Tris, pH 8.5, 1.2 M potassium sodium tartrate tetrahydrate, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.99 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 4, 2008 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.99 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Redundancy: 6.9 % / Number: 213623 / Rmerge(I) obs: 0.074 / Χ2: 2.16 / D res high: 2.45 Å / D res low: 30 Å / Num. obs: 31001 / % possible obs: 99.1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 1.8→50 Å / Num. obs: 79607 / % possible obs: 97.8 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 26.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.309 / Mean I/σ(I) obs: 2.9 |
-Phasing
Phasing | Method: SIRAS |
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-Processing
Software |
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Refinement | Method to determine structure: SIRAS / Resolution: 1.8→33.823 Å / Occupancy max: 1 / Occupancy min: 0.04 / FOM work R set: 0.8577 / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 21.17 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.893 Å2 / ksol: 0.354 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 74.23 Å2 / Biso mean: 27.2666 Å2 / Biso min: 14.64 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→33.823 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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