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- PDB-3c1t: Binding of two substrate analogue molecules to dihydroflavonol 4-... -

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Basic information

Entry
Database: PDB / ID: 3c1t
TitleBinding of two substrate analogue molecules to dihydroflavonol 4-reductase alters the functional geometry of the catalytic site
Componentsdihydroflavonol 4-reductase
KeywordsOXIDOREDUCTASE / short chain dehydrogenase reductase / Rossmann fold / flavonoids
Function / homology
Function and homology information


dihydrokaempferol 4-reductase activity / flavanone 4-reductase activity / dihydroflavonol 4-reductase / flavanone 4-reductase / anthocyanin-containing compound biosynthetic process / 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-MYC / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Dihydroflavonol 4-reductase / Flavanone 4-reductase
Similarity search - Component
Biological speciesVitis vinifera (wine grape)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.252 Å
AuthorsTrabelsi, N. / Petit, P. / Granier, T. / Langlois d'Estaintot, B. / Delrot, S. / Gallois, B.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2008
Title: Structural evidence for the inhibition of grape dihydroflavonol 4-reductase by flavonols
Authors: Trabelsi, N. / Petit, P. / Manigand, C. / Langlois d'Estaintot, B. / Granier, T. / Chaudiere, J. / Gallois, B.
History
DepositionJan 24, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 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_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _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: dihydroflavonol 4-reductase
B: dihydroflavonol 4-reductase
C: dihydroflavonol 4-reductase
D: dihydroflavonol 4-reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,29716
Polymers150,7774
Non-polymers5,52012
Water13,836768
1
A: dihydroflavonol 4-reductase
hetero molecules

C: dihydroflavonol 4-reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,1488
Polymers75,3892
Non-polymers2,7606
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
Buried area6580 Å2
ΔGint-55 kcal/mol
Surface area24520 Å2
MethodPISA
2
B: dihydroflavonol 4-reductase
hetero molecules

D: dihydroflavonol 4-reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,1488
Polymers75,3892
Non-polymers2,7606
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_656x+1,y,z+11
Buried area6700 Å2
ΔGint-61 kcal/mol
Surface area25000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.231, 177.958, 92.597
Angle α, β, γ (deg.)90.00, 104.77, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51A
61B
71C
81D

NCS domain segments:

Ens-ID: 1 / Refine code: 4

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUMETMETAA6 - 886 - 88
21GLUGLUMETMETBB6 - 886 - 88
31GLUGLUMETMETCC6 - 886 - 88
41GLUGLUMETMETDD6 - 886 - 88
52LYSLYSHISHISAA93 - 32993 - 329
62LYSLYSHISHISBB93 - 32993 - 329
72LYSLYSHISHISCC93 - 32993 - 329
82LYSLYSHISHISDD93 - 32993 - 329

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Components

#1: Protein
dihydroflavonol 4-reductase / E.C.1.1.1.219


Mass: 37694.344 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vitis vinifera (wine grape) / Gene: DFR1 / Plasmid: PQE(30XA) / Production host: Escherichia coli (E. coli) / Strain (production host): M15(PREP4)
References: UniProt: P93799, UniProt: P51110*PLUS, dihydroflavonol 4-reductase
#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical
ChemComp-MYC / 3,5,7-TRIHYDROXY-2-(3,4,5-TRIHYDROXYPHENYL)-4H-CHROMEN-4-ONE / 2-(3,4,5-TRIHYDROXYPHENYL)-3,5,7-TRIHYDROXY-4H-1-BENZOPYRAN-4-ONE / 3,3',4',5,5',7-HEXAHYDROXYFLAVONE / MYRICETIN / CANNABISCETIN


Mass: 318.235 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C15H10O8
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 768 / 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: 2.5 Å3/Da / Density % sol: 50.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: NaCl 50 mM, PEG 3350 29%, Hepes 100 mM, NaN3 3 mM, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.04 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 19, 2005 / Details: mirrors
RadiationMonochromator: Si (311) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04 Å / Relative weight: 1
ReflectionResolution: 2.252→89.08 Å / Num. all: 69437 / Num. obs: 69437 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 30 Å2 / Rmerge(I) obs: 0.079 / Rsym value: 0.079 / Net I/σ(I): 5.4
Reflection shellResolution: 2.252→2.37 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.289 / Mean I/σ(I) obs: 2 / Num. unique all: 10024 / Rsym value: 0.289 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.2refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2c29

2c29


Resolution: 2.252→89.09 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.905 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.307 / ESU R Free: 0.241 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25548 3485 5 %RANDOM
Rwork0.18591 ---
all0.18943 65910 --
obs0.18943 65910 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.303 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20 Å2-0.68 Å2
2--1.71 Å20 Å2
3----2.21 Å2
Refine analyzeLuzzati coordinate error obs: 0.254 Å
Refinement stepCycle: LAST / Resolution: 2.252→89.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9981 0 376 768 11125
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02210630
X-RAY DIFFRACTIONr_bond_other_d00.026899
X-RAY DIFFRACTIONr_angle_refined_deg1.9252.00114521
X-RAY DIFFRACTIONr_angle_other_deg4.316316893
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8151297
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.87723.869398
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.464151694
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0341544
X-RAY DIFFRACTIONr_chiral_restr0.1040.21629
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211588
X-RAY DIFFRACTIONr_gen_planes_other0.0070.022071
X-RAY DIFFRACTIONr_nbd_refined0.2110.22474
X-RAY DIFFRACTIONr_nbd_other0.2350.27041
X-RAY DIFFRACTIONr_nbtor_refined0.1870.25165
X-RAY DIFFRACTIONr_nbtor_other0.1130.24804
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1880.2761
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0080.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2190.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1780.244
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2630.213
X-RAY DIFFRACTIONr_mcbond_it2.5681.56474
X-RAY DIFFRACTIONr_mcbond_other01.52599
X-RAY DIFFRACTIONr_mcangle_it3.877210471
X-RAY DIFFRACTIONr_scbond_it2.77834156
X-RAY DIFFRACTIONr_scangle_it3.8284.54048
Refine LS restraints NCS

Ens-ID: 1 / Number: 4077 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.390.5
2Bmedium positional0.360.5
3Cmedium positional0.320.5
4Dmedium positional0.320.5
1Amedium thermal3.232
2Bmedium thermal3.162
3Cmedium thermal2.672
4Dmedium thermal3.512
LS refinement shellResolution: 2.252→2.311 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 250 -
Rwork0.271 4828 -
obs-4828 99.98 %

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