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- PDB-8fen: Panicum vigratum Dihydroflavonol 4-reductase complexed with NADP ... -

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Basic information

Entry
Database: PDB / ID: 8fen
TitlePanicum vigratum Dihydroflavonol 4-reductase complexed with NADP and DHQ
ComponentsPanicum virgatum Dihydroflavonol 4-Reductase
KeywordsOXIDOREDUCTASE / Short Chain Dehydrogenase / Dihydroflavonol 4-reductase / flavonoids / DFR
Function / homologyNAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / NAD(P)-binding domain superfamily / Chem-DQH / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / NAD-dependent epimerase/dehydratase domain-containing protein
Function and homology information
Biological speciesPanicum virgatum (switchgrass)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsLewis, J.A. / Kang, C.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE-1804699 United States
National Science Foundation (NSF, United States)MCB-2043248 United States
CitationJournal: Int J Mol Sci / Year: 2023
Title: Structural Similarities and Overlapping Activities among Dihydroflavonol 4-Reductase, Flavanone 4-Reductase, and Anthocyanidin Reductase Offer Metabolic Flexibility in the Flavonoid Pathway.
Authors: Lewis, J.A. / Zhang, B. / Harza, R. / Palmer, N. / Sarath, G. / Sattler, S.E. / Twigg, P. / Vermerris, W. / Kang, C.
History
DepositionDec 6, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Panicum virgatum Dihydroflavonol 4-Reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4553
Polymers39,4071
Non-polymers1,0482
Water79344
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)119.059, 119.059, 56.988
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein Panicum virgatum Dihydroflavonol 4-Reductase


Mass: 39407.023 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Panicum virgatum (switchgrass) / Gene: PVAP13_5KG450100 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A8T0SQV2
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 1 / 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 / Taxifolin


Mass: 304.252 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H12O7 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.56 Å3/Da / Density % sol: 52 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Tris: HCl, pH 8.5 25 % (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 17, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. obs: 13283 / % possible obs: 98.8 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.2406 / Χ2: 0.137 / Net I/σ(I): 3.7 / Num. measured all: 87458
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.55-2.592.40.87311730.695190.1
2.59-2.642.60.88212710.708199.5
2.64-2.692.80.81912580.909199.8
2.69-2.752.90.8612940.687199.9
2.75-2.813.10.84312570.86199.8
2.81-2.873.30.79413070.731100
2.87-2.943.40.81112540.739199.9
2.94-3.023.50.65913150.7411100
3.02-3.113.60.56612590.73199.9
3.11-3.213.50.51412880.743199.8
3.21-3.333.40.60412881.202199.6
3.33-3.463.20.29812170.814195.5
3.46-3.623.70.27112660.878198.7
3.62-3.8140.24312971.021100
3.81-4.0540.17812810.911100
4.05-4.363.90.14112860.892199.9
4.36-4.840.12812780.954199.8
4.8-5.493.80.10912850.783199.7
5.49-6.923.50.12412360.819196
6.92-504.20.06312861.17198.8

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.20.1_4487refinement
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8FEM

8fem


Resolution: 2.55→37.65 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2382 1329 10.01 %
Rwork0.2152 --
obs0.2175 13282 95.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.55→37.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2515 0 70 44 2629
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005
X-RAY DIFFRACTIONf_angle_d0.611
X-RAY DIFFRACTIONf_dihedral_angle_d16.405952
X-RAY DIFFRACTIONf_chiral_restr0.042403
X-RAY DIFFRACTIONf_plane_restr0.005457
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.650.3161360.28691218X-RAY DIFFRACTION90
2.65-2.770.26851370.26641247X-RAY DIFFRACTION92
2.77-2.920.28581410.25861258X-RAY DIFFRACTION93
2.92-3.10.26171460.24251320X-RAY DIFFRACTION96
3.1-3.340.26921490.24461341X-RAY DIFFRACTION98
3.34-3.670.23731490.22971340X-RAY DIFFRACTION97
3.67-4.20.18521530.18711374X-RAY DIFFRACTION99
4.21-5.290.21711560.17391400X-RAY DIFFRACTION99
5.3-37.650.24281620.20351455X-RAY DIFFRACTION96

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