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Yorodumi- PDB-3i52: Ternary complex structure of leucoanthocyanidin reductase from vi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3i52 | ||||||
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Title | Ternary complex structure of leucoanthocyanidin reductase from vitis vinifera | ||||||
Components | Putative leucoanthocyanidin reductase 1 | ||||||
Keywords | OXIDOREDUCTASE / Rossmann fold / short chain dehydrogenase reductase / flavonoid | ||||||
Function / homology | Function and homology information leucoanthocyanidin reductase / leucoanthocyanidin reductase activity / nucleotide binding Similarity search - Function | ||||||
Biological species | Vitis vinifera (wine grape) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å | ||||||
Authors | Mauge, C. / Gargouri, M. / d'Estaintot, B.L. / Granier, T. / Gallois, B. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2010 Title: Crystal structure and catalytic mechanism of leucoanthocyanidin reductase from Vitis vinifera. Authors: Mauge, C. / Granier, T. / d'Estaintot, B.L. / Gargouri, M. / Manigand, C. / Schmitter, J.M. / Chaudiere, J. / Gallois, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3i52.cif.gz | 78.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3i52.ent.gz | 56.8 KB | Display | PDB format |
PDBx/mmJSON format | 3i52.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i5/3i52 ftp://data.pdbj.org/pub/pdb/validation_reports/i5/3i52 | HTTPS FTP |
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-Related structure data
Related structure data | 3i5mC 3i6iC 3i6qC 3cjv C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 38060.445 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vitis vinifera (wine grape) / Gene: lar1 / Plasmid: PETGB1A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21[DE3] / References: UniProt: Q4W2K4, leucoanthocyanidin reductase |
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#2: Chemical | ChemComp-NAP / |
#3: Chemical | ChemComp-KXN / ( |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 40.11 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: Sodium acetate 0.3M, PEG 4000 32.5%, TRIS HCL 0.1M, Glycerol 2.5%, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 3, 2008 Details: Pt coated mirrors in a Kirkpatrick-Baez (KB) geometry |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 2.28→40.59 Å / Num. all: 13391 / Num. obs: 13391 / % possible obs: 93.85 % / Redundancy: 2.4 % / Biso Wilson estimate: 29.25 Å2 / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 7.5 |
Reflection shell | Resolution: 2.28→2.4 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.338 / Mean I/σ(I) obs: 2 / Num. unique all: 1979 / Rsym value: 0.338 / % possible all: 97.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3cjv 3cjv Resolution: 2.28→40.59 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.925 / SU B: 12.109 / SU ML: 0.141 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic + TLS / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.33 / ESU R Free: 0.224 / 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.066 Å2
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Refinement step | Cycle: LAST / Resolution: 2.28→40.59 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.28→2.339 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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