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- PDB-3i5m: Structure of the apo form of leucoanthocyanidin reductase from vi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3i5m | ||||||
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Title | Structure of the apo form of leucoanthocyanidin reductase from vitis vinifera | ||||||
![]() | Putative leucoanthocyanidin reductase 1 | ||||||
![]() | OXIDOREDUCTASE / Rossmann fold / short chain dehydrogenase reductase / flavonoid | ||||||
Function / homology | ![]() leucoanthocyanidin reductase / leucoanthocyanidin reductase activity / nucleotide binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Mauge, C. / Gargouri, M. / d'Estaintot, B.L. / Granier, T. / Gallois, B. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 70.8 KB | Display | ![]() |
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PDB format | ![]() | 51.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 413.2 KB | Display | ![]() |
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Full document | ![]() | 414 KB | Display | |
Data in XML | ![]() | 12.4 KB | Display | |
Data in CIF | ![]() | 16.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3i52SC ![]() 3i6iC ![]() 3i6qC 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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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.) ![]() ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.66 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: PEG 4000 35%, sodium acetate 340mM, Tris 0.1M, sodium azide 3mM, glycerol 3.5%, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 7, 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: 2.72→66.23 Å / Num. all: 7546 / Num. obs: 7546 / % possible obs: 90 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Biso Wilson estimate: 44 Å2 / Rmerge(I) obs: 0.107 / Net I/σ(I): 5 |
Reflection shell | Resolution: 2.72→2.87 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.294 / Mean I/σ(I) obs: 2 / Num. unique all: 1132 / % possible all: 92.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3I52 Resolution: 2.72→66.23 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.898 / SU B: 26.409 / SU ML: 0.249 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.386 / 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: 15.696 Å2
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Refinement step | Cycle: LAST / Resolution: 2.72→66.23 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.72→2.791 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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