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Yorodumi- PDB-2e1v: Crystal structure of Dendranthema morifolium DmAT, seleno-methion... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2e1v | ||||||
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Title | Crystal structure of Dendranthema morifolium DmAT, seleno-methionine derivative | ||||||
Components | acyl transferase | ||||||
Keywords | TRANSFERASE / BAHD superfamily / acyl transferase / seleno-methionine derivative / Dendranthema morifolium / DmAT | ||||||
Function / homology | Transferase family / Chloramphenicol Acetyltransferase / Chloramphenicol acetyltransferase-like domain / Chloramphenicol acetyltransferase-like domain superfamily / transferase activity / 2-Layer Sandwich / Alpha Beta / Anthocyanin malonyltransferase homolog Function and homology information | ||||||
Biological species | Chrysanthemum x morifolium (florist's chrysanthemum) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å | ||||||
Authors | Unno, H. / Ichimaida, F. / Kusunoki, M. / Nakayama, T. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2007 Title: Structural and Mutational Studies of Anthocyanin Malonyltransferases Establish the Features of BAHD Enzyme Catalysis Authors: Unno, H. / Ichimaida, F. / Suzuki, H. / Takahashi, S. / Tanaka, Y. / Saito, A. / Nishino, T. / Kusunoki, M. / Nakayama, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2e1v.cif.gz | 197.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2e1v.ent.gz | 165 KB | Display | PDB format |
PDBx/mmJSON format | 2e1v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e1/2e1v ftp://data.pdbj.org/pub/pdb/validation_reports/e1/2e1v | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1 / Refine code: 3
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-Components
#1: Protein | Mass: 51235.379 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chrysanthemum x morifolium (florist's chrysanthemum) Plasmid: pET15b / Production host: Escherichia coli (E. coli) / References: UniProt: A4PHY4, Transferases #2: 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: 2.22 Å3/Da / Density % sol: 44.55 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 20% PEG 3350, 20% glycerol, 0.2M magnesium chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 90 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 0.97909, 0.97928, 0.95000 | ||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 2, 2006 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.8→50 Å / Num. obs: 81316 / % possible obs: 98.6 % / Redundancy: 7.9 % / Biso Wilson estimate: 24.275 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 31.4 | ||||||||||||
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.276 / Mean I/σ(I) obs: 5.3 / % possible all: 93 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.8→30.46 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.937 / SU B: 2.924 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.149 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.726 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→30.46 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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