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- PDB-2nnl: Binding of two substrate analogue molecules to dihydroflavonol-4-... -

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Basic information

Entry
Database: PDB / ID: 2nnl
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


dihydroflavonol 4-reductase / dihydrokaempferol 4-reductase activity / flavanone 4-reductase activity / flavanone 4-reductase / anthocyanin-containing compound 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-ERD / 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: 2.1 Å
AuthorsPetit, P. / Langlois D'Estaintot, B. / Granier, T. / Gallois, B.
CitationJournal: To be Published
Title: Binding of two substrate analogue molecules to dihydroflavonol-4-reductase alters the functional geometry of the catalytic site
Authors: Petit, P. / Langlois D'Estaintot, B. / Granier, T. / Gallois, B.
History
DepositionOct 24, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 13, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 25, 2019Group: Data collection / Category: reflns_shell
Item: _reflns_shell.Rmerge_I_obs / _reflns_shell.pdbx_Rsym_value
Revision 1.3Oct 25, 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.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_seq_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

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Assembly

Deposited unit
D: Dihydroflavonol 4-reductase
F: Dihydroflavonol 4-reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,4526
Polymers75,3892
Non-polymers2,0634
Water10,052558
1
D: Dihydroflavonol 4-reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7263
Polymers37,6941
Non-polymers1,0322
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
F: Dihydroflavonol 4-reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7263
Polymers37,6941
Non-polymers1,0322
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.825, 90.143, 93.297
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11D
21F
12D
22F
13D
23F
14D
24F
15D
25F
16D
26F

NCS domain segments:

Component-ID: 1 / Refine code: 2

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUILEILEDA6 - 1106 - 110
21GLUGLUILEILEFB6 - 1106 - 110
12GLYGLYTYRTYRDA130 - 177130 - 177
22GLYGLYTYRTYRFB130 - 177130 - 177
13ASPASPLEULEUDA184 - 261184 - 261
23ASPASPLEULEUFB184 - 261184 - 261
14TYRTYRHISHISDA271 - 329271 - 329
24TYRTYRHISHISFB271 - 329271 - 329
15NAPNAPNAPNAPDC1330
25NAPNAPNAPNAPFE2330
16ERDERDERDERDDD1331
26ERDERDERDERDFF2331

NCS ensembles :
ID
1
2
3
4
5
6

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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
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.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-ERD / (2S)-2-(3,4-DIHYDROXYPHENYL)-5,7-DIHYDROXY-2,3-DIHYDRO-4H-CHROMEN-4-ONE


Mass: 288.252 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H12O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 558 / 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: 2.45 Å3/Da / Density % sol: 49.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: 50MM NACL, 29% PEG3350, 100MM HEPES, 3MM NAN3, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.04 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 5, 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: 2.1→64.827 Å / Num. all: 37210 / Num. obs: 37210 / % possible obs: 85.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Biso Wilson estimate: 34.4 Å2 / Rmerge(I) obs: 0.136 / Rsym value: 0.136 / Net I/σ(I): 3.7
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 5.3 % / Mean I/σ(I) obs: 1.9 / Num. measured all: 29478 / Num. unique all: 5566 / % possible all: 89.1

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
ADSCQuantumdata collection
MOSFLMdata reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2c29

2c29


Resolution: 2.1→64.82 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.937 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.291 / ESU R Free: 0.221 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.242 1899 5.1 %RANDOM
Rwork0.19 ---
all0.192 37159 --
obs0.192 37159 84.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.017 Å2
Baniso -1Baniso -2Baniso -3
1--0.33 Å20 Å20 Å2
2--2.47 Å20 Å2
3----2.14 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 2.1→64.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5027 0 138 558 5723
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0225301
X-RAY DIFFRACTIONr_angle_refined_deg1.2711.9897234
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1875656
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.56223.869199
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.50915851
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.111522
X-RAY DIFFRACTIONr_chiral_restr0.0840.2822
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023931
X-RAY DIFFRACTIONr_nbd_refined0.1910.22506
X-RAY DIFFRACTIONr_nbtor_refined0.3040.23640
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2514
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1890.256
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.150.212
X-RAY DIFFRACTIONr_mcbond_it1.51933268
X-RAY DIFFRACTIONr_mcangle_it2.53465291
X-RAY DIFFRACTIONr_scbond_it1.68332033
X-RAY DIFFRACTIONr_scangle_it2.53761943
Refine LS restraints NCS

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

Ens-IDNumberTypeRms dev position (Å)Weight position
1412TIGHT POSITIONAL0.040.05
1359MEDIUM POSITIONAL0.330.5
1412TIGHT THERMAL0.862
1359MEDIUM THERMAL1.444
2192TIGHT POSITIONAL0.030.05
2203MEDIUM POSITIONAL0.210.5
2192TIGHT THERMAL0.872
2203MEDIUM THERMAL1.234
3312TIGHT POSITIONAL0.040.05
3292MEDIUM POSITIONAL0.170.5
3312TIGHT THERMAL1.082
3292MEDIUM THERMAL1.594
4240TIGHT POSITIONAL0.040.05
4221MEDIUM POSITIONAL0.240.5
4240TIGHT THERMAL1.12
4221MEDIUM THERMAL1.514
548MEDIUM POSITIONAL0.090.5
548MEDIUM THERMAL1.194
621MEDIUM POSITIONAL0.040.5
621MEDIUM THERMAL1.454
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 155 -
Rwork0.289 2650 -
obs-2805 88.63 %

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