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- PDB-8feu: Flavanone 4-Reductase from Sorghum bicolor-NADP(H) and naringenin... -

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Basic information

Entry
Database: PDB / ID: 8feu
TitleFlavanone 4-Reductase from Sorghum bicolor-NADP(H) and naringenin complex
Components3-deoxyanthocyanidin synthase
KeywordsOXIDOREDUCTASE / SDR type protein / flavanone / sorghum
Function / homology: / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / NAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / NAD(P)-binding domain superfamily / nucleotide binding / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / NARINGENIN / 3-deoxyanthocyanidin synthase
Function and homology information
Biological speciesSorghum bicolor (sorghum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 Å
AuthorsZhang, B. / 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: 3-deoxyanthocyanidin synthase
B: 3-deoxyanthocyanidin synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,10210
Polymers75,6862
Non-polymers2,4168
Water7,224401
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)165.180, 165.180, 207.655
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-706-

HOH

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Components

#1: Protein 3-deoxyanthocyanidin synthase


Mass: 37843.082 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sorghum bicolor (sorghum) / Production host: Escherichia coli (E. coli) / References: UniProt: C5YGL7
#2: Chemical ChemComp-NAR / NARINGENIN


Mass: 272.253 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H12O5 / Feature type: SUBJECT OF INVESTIGATION
#3: 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 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 401 / 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: 4.68 Å3/Da / Density % sol: 73.71 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.1 M HEPES, pH 7.5, 2 M Ammonium Sulfate and 2 % PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 13, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 2.12→47.44 Å / Num. obs: 80982 / % possible obs: 99.97 % / Redundancy: 2 % / CC1/2: 0.999 / Net I/σ(I): 17.62
Reflection shellResolution: 2.12→2.196 Å / Num. unique obs: 15966 / CC1/2: 0.7037

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Processing

Software
NameVersionClassification
XDSdata reduction
PHENIX1.2refinement
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.12→47.44 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2266 2000 2.47 %
Rwork0.1988 --
obs0.1995 80973 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.12→47.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5170 0 156 401 5727
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007
X-RAY DIFFRACTIONf_angle_d0.9
X-RAY DIFFRACTIONf_dihedral_angle_d8.844738
X-RAY DIFFRACTIONf_chiral_restr0.053832
X-RAY DIFFRACTIONf_plane_restr0.008940
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.12-2.170.34911410.32575579X-RAY DIFFRACTION100
2.17-2.230.361420.29775576X-RAY DIFFRACTION100
2.23-2.30.2511400.28215556X-RAY DIFFRACTION100
2.3-2.370.36521410.27615584X-RAY DIFFRACTION100
2.37-2.460.30261410.26545562X-RAY DIFFRACTION100
2.46-2.550.25231430.24415626X-RAY DIFFRACTION100
2.55-2.670.28041410.23465588X-RAY DIFFRACTION100
2.67-2.810.27171430.22745622X-RAY DIFFRACTION100
2.81-2.990.25911420.23295618X-RAY DIFFRACTION100
2.99-3.220.26671420.21735628X-RAY DIFFRACTION100
3.22-3.540.21641440.19675676X-RAY DIFFRACTION100
3.54-4.050.20361440.17215671X-RAY DIFFRACTION100
4.05-5.110.17471460.14865741X-RAY DIFFRACTION100
5.11-47.440.18441500.16615946X-RAY DIFFRACTION100

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