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Yorodumi- PDB-3i6i: Structure of the binary complex leucoanthocyanidin reductase - NA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3i6i | ||||||
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Title | Structure of the binary complex leucoanthocyanidin reductase - NADPH 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: 1.75 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 | 3i6i.cif.gz | 81.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3i6i.ent.gz | 59 KB | Display | PDB format |
PDBx/mmJSON format | 3i6i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i6/3i6i ftp://data.pdbj.org/pub/pdb/validation_reports/i6/3i6i | HTTPS FTP |
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-Related structure data
Related structure data | 3i52SC 3i5mC 3i6qC S: Starting model for refinement C: citing same article (ref.) |
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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-NDP / |
#3: Chemical | ChemComp-ACY / |
#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: 1.95 Å3/Da / Density % sol: 36.92 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: Sodium acetate 0.36M, PEG 4000 38%, Tris 100mM, NaN3 3mM, glycerol 2.5%, pH 8.5, 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: Nov 8, 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: 1.75→65.51 Å / Num. all: 28119 / Num. obs: 28119 / % possible obs: 94.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 15.161 Å2 / Rsym value: 0.077 / Net I/σ(I): 6.7 |
Reflection shell | Resolution: 1.75→1.84 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 2 / Num. unique all: 4067 / Rsym value: 0.339 / % possible all: 94.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3I52 Resolution: 1.75→40.62 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.94 / SU B: 4.965 / SU ML: 0.072 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.112 / ESU R Free: 0.112 / Stereochemistry target values: Engh & Huber / 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: 6.987 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→40.62 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.795 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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