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

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Basic information

Entry
Database: PDB / ID: 3bxx
TitleBinding of two substrate analogue molecules to dihydroflavonol 4-reductase alters the functional geometry of the catalytic site
Componentsdihydroflavonol 4-reductase
KeywordsOXIDOREDUCTASE / rossmann fold
Function / homology
Function and homology information


dihydroflavanol 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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 3,5,7,3',4'-PENTAHYDROXYFLAVONE / Dihydroflavonol 4-reductase / Flavanone 4-reductase
Similarity search - Component
Biological speciesVitis vinifera (wine grape)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.9 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 15, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: 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 / refine_ls_restr_ncs / 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 / _refine_ls_restr_ncs.pdbx_auth_asym_id / _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
E: dihydroflavonol 4-reductase
F: dihydroflavonol 4-reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)233,34721
Polymers226,1666
Non-polymers7,18115
Water2,324129
1
A: dihydroflavonol 4-reductase
D: dihydroflavonol 4-reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,7827
Polymers75,3892
Non-polymers2,3945
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7590 Å2
ΔGint-46 kcal/mol
Surface area25220 Å2
MethodPISA
2
B: dihydroflavonol 4-reductase
C: dihydroflavonol 4-reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,0848
Polymers75,3892
Non-polymers2,6966
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8010 Å2
ΔGint-51 kcal/mol
Surface area24830 Å2
MethodPISA
3
E: dihydroflavonol 4-reductase
F: dihydroflavonol 4-reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,4806
Polymers75,3892
Non-polymers2,0914
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6710 Å2
ΔGint-35 kcal/mol
Surface area25420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)174.943, 174.943, 290.167
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
12A
22B
32C
42D
52E
62F

NCS domain segments:

Component-ID: 1 / Refine code: 4

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUGLUGLUAA6 - 916 - 91
21GLUGLUGLUGLUBB6 - 916 - 91
31GLUGLUGLUGLUCC6 - 916 - 91
41GLUGLUGLUGLUDD6 - 916 - 91
51GLUGLUGLUGLUEE6 - 916 - 91
61GLUGLUGLUGLUFF6 - 916 - 91
12LYSLYSHISHISAA93 - 32993 - 329
22LYSLYSHISHISBB93 - 32993 - 329
32LYSLYSHISHISCC93 - 32993 - 329
42LYSLYSHISHISDD93 - 32993 - 329
52LYSLYSHISHISEE93 - 32993 - 329
62LYSLYSHISHISFF93 - 32993 - 329

NCS ensembles :
ID
1
2

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Components

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


Mass: 37694.344 Da / Num. of mol.: 6
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.: 6 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical
ChemComp-QUE / 3,5,7,3',4'-PENTAHYDROXYFLAVONE / QUERCETIN


Mass: 302.236 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C15H10O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 2.83 Å3/Da / Density % sol: 56.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: NaCl 130 mM, 35% PEG 3350, 100 mM Hepes 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: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 17, 2006 / Details: mirrors
RadiationMonochromator: Ge (220) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.9→75.81 Å / Num. obs: 58753 / % possible obs: 100 % / Redundancy: 14.3 % / Rmerge(I) obs: 0.153 / Rsym value: 0.153 / Net I/σ(I): 4.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.9-3.0614.20.4251.711989184280.425100
3.06-3.2414.40.3382.111471479820.338100
3.24-3.4714.60.239310950975120.239100
3.47-3.7414.70.1723.310300670190.172100
3.74-4.114.60.125.49492964960.12100
4.1-4.5914.50.0986.28600459130.098100
4.59-5.2914.40.0926.27559652530.092100
5.29-6.4814.20.0985.96343844800.098100
6.48-9.1713.70.0746.44881335600.074100
9.17-75.8111.90.0615.72505521100.06199.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.004data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→75.81 Å / Cor.coef. Fo:Fc: 0.881 / Cor.coef. Fo:Fc free: 0.796 / SU B: 22.851 / SU ML: 0.453 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.576 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.366 2967 5.1 %RANDOM
Rwork0.288 ---
obs0.292 58667 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 22.069 Å2
Baniso -1Baniso -2Baniso -3
1-0.41 Å20.21 Å20 Å2
2--0.41 Å20 Å2
3----0.62 Å2
Refinement stepCycle: LAST / Resolution: 2.9→75.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15182 0 486 129 15797
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02216070
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210673
X-RAY DIFFRACTIONr_angle_refined_deg2.3311.99921877
X-RAY DIFFRACTIONr_angle_other_deg1.44326126
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.12851938
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.89124.086629
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.184152686
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8451566
X-RAY DIFFRACTIONr_chiral_restr0.1220.22436
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0217408
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023129
X-RAY DIFFRACTIONr_nbd_refined0.2250.24175
X-RAY DIFFRACTIONr_nbd_other0.1880.210983
X-RAY DIFFRACTIONr_nbtor_refined0.190.27518
X-RAY DIFFRACTIONr_nbtor_other0.0870.28321
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2010.2543
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0960.25
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2620.227
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1610.268
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1140.25
X-RAY DIFFRACTIONr_mcbond_it1.234210140
X-RAY DIFFRACTIONr_mcbond_other0.16123894
X-RAY DIFFRACTIONr_mcangle_it2.08615713
X-RAY DIFFRACTIONr_scbond_it0.82327445
X-RAY DIFFRACTIONr_scangle_it1.31566164
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAsym-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11AA1098MEDIUM POSITIONAL0.420.5
12BB1098MEDIUM POSITIONAL0.520.5
13CC1098MEDIUM POSITIONAL0.50.5
14DD1098MEDIUM POSITIONAL0.580.5
15EE1098MEDIUM POSITIONAL0.590.5
16FF1098MEDIUM POSITIONAL0.450.5
11AA1098MEDIUM THERMAL2.978
12BB1098MEDIUM THERMAL5.218
13CC1098MEDIUM THERMAL5.848
14DD1098MEDIUM THERMAL2.888
15EE1098MEDIUM THERMAL4.348
16FF1098MEDIUM THERMAL2.658
21AA3146MEDIUM POSITIONAL0.450.5
22BB3146MEDIUM POSITIONAL0.460.5
23CC3146MEDIUM POSITIONAL0.420.5
24DD3146MEDIUM POSITIONAL0.560.5
25EE3146MEDIUM POSITIONAL0.570.5
26FF3146MEDIUM POSITIONAL0.50.5
21AA3146MEDIUM THERMAL3.038
22BB3146MEDIUM THERMAL5.528
23CC3146MEDIUM THERMAL5.938
24DD3146MEDIUM THERMAL3.188
25EE3146MEDIUM THERMAL3.838
26FF3146MEDIUM THERMAL2.918
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.46 197 -
Rwork0.282 4079 -
all-4276 -
obs--100 %

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