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- PDB-3i52: Ternary complex structure of leucoanthocyanidin reductase from vi... -

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Basic information

Entry
Database: PDB / ID: 3i52
TitleTernary complex structure 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
Chem-KXN / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Leucoanthocyanidin reductase 1
Similarity search - Component
Biological speciesVitis vinifera (wine grape)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 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 3, 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative leucoanthocyanidin reductase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0943
Polymers38,0601
Non-polymers1,0342
Water2,972165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.681, 50.870, 68.961
Angle α, β, γ (deg.)90.00, 102.71, 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: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-KXN / (2R,3S)-2-(3,4-dihydroxyphenyl)-3,4-dihydro-2H-chromene-3,5,7-triol


Mass: 290.268 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H14O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 2.05 Å3/Da / Density % sol: 40.11 %
Crystal growTemperature: 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

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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: Jun 3, 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: 2.28→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 shellResolution: 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

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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: 3cjv

3cjv
PDB Unreleased entry


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
RfactorNum. reflection% reflectionSelection details
Rfree0.21196 675 5 %RANDOM
Rwork0.14198 ---
all0.14537 13391 --
obs0.14537 12715 93.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.066 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å2-0.19 Å2
2---0.02 Å20 Å2
3----0.08 Å2
Refinement stepCycle: LAST / Resolution: 2.28→40.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2275 0 69 165 2509
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222415
X-RAY DIFFRACTIONr_bond_other_d0.0020.021578
X-RAY DIFFRACTIONr_angle_refined_deg1.4851.9863298
X-RAY DIFFRACTIONr_angle_other_deg2.2933849
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3145298
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.92923.824102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.98815373
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5391514
X-RAY DIFFRACTIONr_chiral_restr0.0840.2376
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212660
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02488
X-RAY DIFFRACTIONr_mcbond_it2.53941479
X-RAY DIFFRACTIONr_mcbond_other0.3074601
X-RAY DIFFRACTIONr_mcangle_it3.76482401
X-RAY DIFFRACTIONr_scbond_it4.496936
X-RAY DIFFRACTIONr_scangle_it6.14412896
LS refinement shellResolution: 2.28→2.339 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 53 -
Rwork0.151 932 -
obs-932 96.95 %
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)
13.7106-0.3172-0.23812.7593-0.48431.6624-0.185-1.32880.73530.68030.1344-0.131-0.28190.04740.05060.19440.0741-0.05720.4768-0.26640.157814.64611.3821.615
25.27290.90280.28971.88380.18880.2112-0.0147-0.52390.13270.2439-0.01060.1874-0.03-0.05460.02530.07410.01150.07050.1291-0.02050.11043.543.1519.021
35.59430.55380.5811.0077-0.10720.96450.0249-0.7334-0.42720.13660.00910.10460.013-0.0909-0.03390.06120.00630.08620.12760.06460.1635-1.568-8.08311.854
47.89781.7342-1.13242.3154-1.032.91410.2356-1.4342-0.61170.2895-0.09840.0955-0.01250.0106-0.13710.0626-0.00910.05750.3180.17740.22279.104-12.08218.722
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 118
2X-RAY DIFFRACTION2A119 - 177
3X-RAY DIFFRACTION3A178 - 290
4X-RAY DIFFRACTION4A291 - 317

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