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- PDB-8fet: Flavanone 4-Reductase from Sorghum bicolor-NADP(H) complex -

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Basic information

Entry
Database: PDB / ID: 8fet
TitleFlavanone 4-Reductase from Sorghum bicolor-NADP(H) 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 / 3-deoxyanthocyanidin synthase
Function and homology information
Biological speciesSorghum bicolor (sorghum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.202 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)77,1734
Polymers75,6862
Non-polymers1,4872
Water5,675315
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)163.203, 163.203, 206.566
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-659-

HOH

21A-672-

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-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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 315 / 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: 4.54 Å3/Da / Density % sol: 72.93 %
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: 1 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Mar 31, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.202→47.14 Å / Num. obs: 70362 / % possible obs: 99.34 % / Redundancy: 13.1 % / CC1/2: 0.999 / Net I/σ(I): 13.96
Reflection shellResolution: 2.202→2.28 Å / Num. unique obs: 6871 / CC1/2: 0.724 / % possible all: 98.61

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Processing

Software
NameVersionClassification
HKL-2000data reduction
PHENIX1.2refinement
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.202→47.14 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2319 2000 2.86 %
Rwork0.2067 --
obs0.2075 69933 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.202→47.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5170 0 96 315 5581
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065378
X-RAY DIFFRACTIONf_angle_d0.8787312
X-RAY DIFFRACTIONf_dihedral_angle_d8.043734
X-RAY DIFFRACTIONf_chiral_restr0.049830
X-RAY DIFFRACTIONf_plane_restr0.007934
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.202-2.260.35771390.31784755X-RAY DIFFRACTION99
2.26-2.320.39341420.31574772X-RAY DIFFRACTION99
2.32-2.390.32431400.29554767X-RAY DIFFRACTION99
2.39-2.460.36351410.29474787X-RAY DIFFRACTION99
2.46-2.550.35971420.28764806X-RAY DIFFRACTION99
2.55-2.650.31811400.28264783X-RAY DIFFRACTION99
2.65-2.770.32521420.26534821X-RAY DIFFRACTION99
2.77-2.920.30191420.26264843X-RAY DIFFRACTION100
2.92-3.10.25921430.2574843X-RAY DIFFRACTION100
3.1-3.340.26351430.23174852X-RAY DIFFRACTION100
3.34-3.680.22851440.19954885X-RAY DIFFRACTION100
3.68-4.210.18161440.17134899X-RAY DIFFRACTION100
4.21-5.30.17061460.1514969X-RAY DIFFRACTION100
5.3-47.140.17531520.16695151X-RAY DIFFRACTION100

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