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- PDB-3i5m: Structure of the apo form of leucoanthocyanidin reductase from vi... -

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Basic information

Entry
Database: PDB / ID: 3i5m
TitleStructure of the apo form of leucoanthocyanidin reductase from vitis vinifera
ComponentsPutative leucoanthocyanidin reductase 1
KeywordsOXIDOREDUCTASE / Rossmann fold / short chain dehydrogenase reductase / flavonoid
Function / homology
Function and homology information


leucoanthocyanidin reductase / leucoanthocyanidin reductase activity / nucleotide binding
Similarity search - Function
Phenylcoumaran benzylic ether reductase-like / : / NmrA-like domain / NmrA-like family / UDP-galactose 4-epimerase, domain 1 / UDP-galactose 4-epimerase; domain 1 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold ...Phenylcoumaran benzylic ether reductase-like / : / NmrA-like domain / NmrA-like family / UDP-galactose 4-epimerase, domain 1 / UDP-galactose 4-epimerase; domain 1 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Leucoanthocyanidin reductase 1
Similarity search - Component
Biological speciesVitis vinifera (wine grape)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.72 Å
AuthorsMauge, C. / Gargouri, M. / d'Estaintot, B.L. / Granier, T. / Gallois, B.
CitationJournal: 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
DepositionJul 6, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 20, 2013Group: Database references
Revision 1.3Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative leucoanthocyanidin reductase 1


Theoretical massNumber of molelcules
Total (without water)38,0601
Polymers38,0601
Non-polymers00
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.421, 50.715, 68.051
Angle α, β, γ (deg.)90.00, 103.18, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Putative leucoanthocyanidin reductase 1


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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.01 Å3/Da / Density % sol: 38.66 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 7, 2008
Details: Pt coated mirrors in a Kirkpatrick-Baez (KB) geometry
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

Software
NameVersionClassification
DNAdata collection
MOLREPphasing
REFMAC5.5.0072refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3I52

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
RfactorNum. reflection% reflectionSelection details
Rfree0.23453 350 4.7 %RANDOM
Rwork0.17104 ---
all0.17426 7060 --
obs0.17426 7060 89.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.696 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20 Å20.73 Å2
2---0.58 Å20 Å2
3---0.76 Å2
Refinement stepCycle: LAST / Resolution: 2.72→66.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2276 0 0 47 2323
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222330
X-RAY DIFFRACTIONr_angle_refined_deg1.3321.9533171
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8145302
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.80823.77698
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.27415360
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9591514
X-RAY DIFFRACTIONr_chiral_restr0.090.2364
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211780
X-RAY DIFFRACTIONr_mcbond_it0.4391.51496
X-RAY DIFFRACTIONr_mcangle_it0.86222416
X-RAY DIFFRACTIONr_scbond_it1.413834
X-RAY DIFFRACTIONr_scangle_it2.3924.5754
LS refinement shellResolution: 2.72→2.791 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 41 -
Rwork0.198 506 -
obs-506 92.55 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.39750.16310.60693.4397-0.56273.9581-0.0334-0.53260.33790.641-0.02950.1096-0.3428-0.05280.06280.2409-0.00370.01640.1691-0.05850.140313.13910.69121.742
22.80780.55320.81363.277-0.39721.24950.0959-0.04540.02860.140.01320.30770.0021-0.1814-0.1090.04250.026-0.01190.0661-0.0130.09963.7663.6378.292
34.3030.74120.62461.2262-0.19190.829-0.0724-0.1999-0.11960.15690.02790.1178-0.0402-0.10360.04460.08360.0070.02370.037-0.01860.06530.072-8.4311.457
49.9345-0.4534-2.30194.61380.17726.3020.3213-1.58690.66760.644-0.3041-0.0705-0.3403-0.1002-0.01730.2948-0.07050.0220.3533-0.00910.40063.197-14.27924.416
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 125
2X-RAY DIFFRACTION2A126 - 178
3X-RAY DIFFRACTION3A179 - 300
4X-RAY DIFFRACTION4A301 - 317

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