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- PDB-2c29: Structure of dihydroflavonol reductase from Vitis vinifera at 1.8 A. -

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Basic information

Entry
Database: PDB / ID: 2c29
TitleStructure of dihydroflavonol reductase from Vitis vinifera at 1.8 A.
ComponentsDIHYDROFLAVONOL 4-REDUCTASE
KeywordsOXIDOREDUCTASE / FLAVONOIDS / SHORT DEHYDROGENASE REDUCTASE / NADPH / DIHYDROQUERCETIN / ROSSMANN FOLD
Function / homology
Function and homology information


dihydroflavanol 4-reductase activity / dihydroflavonol 4-reductase / flavanone 4-reductase / flavonoid biosynthetic process / nucleotide binding
Similarity search - Function
: / NAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-DQH / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Flavanone 4-reductase
Similarity search - Component
Biological speciesVITIS VINIFERA (wine grape)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.81 Å
AuthorsPetit, P. / Granier, T. / D'Estaintot, B.L. / Hamdi, S. / Gallois, B.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Crystal Structure of Grape Dihydroflavonol 4-Reductase, a Key Enzyme in Flavonoid Biosynthesis.
Authors: Petit, P. / Granier, T. / D'Estaintot, B.L. / Manigand, C. / Bathany, K. / Schmitter, J.M. / Lauvergeat, V. / Hamdi, S. / Gallois, B.
History
DepositionSep 27, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 16, 2006Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: DIHYDROFLAVONOL 4-REDUCTASE
F: DIHYDROFLAVONOL 4-REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,4846
Polymers75,3892
Non-polymers2,0954
Water10,377576
1
D: DIHYDROFLAVONOL 4-REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7423
Polymers37,6941
Non-polymers1,0482
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
F: DIHYDROFLAVONOL 4-REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7423
Polymers37,6941
Non-polymers1,0482
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)87.818, 89.927, 93.191
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11D
21F

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1115D6 - 110
2115F6 - 110
1215D130 - 177
2215F130 - 177
1315D184 - 261
2315F184 - 261
1415D271 - 329
2415F271 - 329
1511D332 - 333
2511F332 - 333

NCS oper: (Code: given
Matrix: (-0.03694, -0.99926, 0.01094), (-0.99928, 0.03703, 0.00793), (-0.00833, -0.01064, -0.99991)
Vector: 115.17899, 106.01623, 69.9229)

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Components

#1: Protein DIHYDROFLAVONOL 4-REDUCTASE


Mass: 37694.344 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: ROSSMANN FOLD / Source: (gene. exp.) VITIS VINIFERA (wine grape) / Plasmid: PQE(30XA) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): M15(PREP4) / References: UniProt: P93799, dihydroflavonol 4-reductase
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-DQH / (2R,3R)-2-(3,4-DIHYDROXYPHENYL)-3,5,7-TRIHYDROXY-2,3-DIHYDRO-4H-CHROMEN-4-ONE / (2R,3R)-TRANS-DIHYDROQUERCETIN


Mass: 304.252 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H12O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 576 / 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: 2.29 Å3/Da / Density % sol: 45.83 %
Crystal growpH: 7.5 / Details: NACL 80-200MM PEG 3350 25-30% HEPES 100MM PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.97319
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 5, 2005 / Details: MIRRORS
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97319 Å / Relative weight: 1
ReflectionResolution: 1.81→1.91 Å / Num. obs: 66981 / % possible obs: 98.9 % / Observed criterion σ(I): 2 / Redundancy: 5.3 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 6.7
Reflection shellResolution: 1.81→1.91 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2 / % possible all: 98.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 1.81→16.43 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.939 / Cross valid method: THROUGHOUT / ESU R: 0.134 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.244 3382 5.1 %RANDOM
Rwork0.192 ---
obs0.195 63444 98.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.43 Å2
Baniso -1Baniso -2Baniso -3
1--0.68 Å20 Å20 Å2
2--3.49 Å20 Å2
3----2.81 Å2
Refinement stepCycle: LAST / Resolution: 1.81→16.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4990 0 140 576 5706
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0225303
X-RAY DIFFRACTIONr_bond_other_d00.024709
X-RAY DIFFRACTIONr_angle_refined_deg1.4281.9897238
X-RAY DIFFRACTIONr_angle_other_deg3.751310955
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5985656
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.84523.869199
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.05715851
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.4331522
X-RAY DIFFRACTIONr_chiral_restr0.0810.2824
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025801
X-RAY DIFFRACTIONr_gen_planes_other0.0070.021044
X-RAY DIFFRACTIONr_nbd_refined0.2020.21119
X-RAY DIFFRACTIONr_nbd_other0.2250.24414
X-RAY DIFFRACTIONr_nbtor_refined0.1780.22564
X-RAY DIFFRACTIONr_nbtor_other0.1090.22332
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.2475
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1160.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1660.254
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1310.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.2733268
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.3365291
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.64632035
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.63361947
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: D / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
97tight positional0.060.05
1699medium positional0.140.5
2587loose positional0.375
97tight thermal0.260.5
1699medium thermal1.692
2587loose thermal2.6910
LS refinement shellResolution: 1.81→1.86 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.376 234
Rwork0.341 4378

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