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- PDB-7d3b: flavone reductase -

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Basic information

Entry
Database: PDB / ID: 7d3b
Titleflavone reductase
ComponentsCd1
KeywordsFLAVOPROTEIN / flavone reductase / FMN / Luteolin
Function / homologyNADPH-dependent FMN reductase-like / NADPH-dependent FMN reductase / Flavoprotein-like superfamily / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / FLAVIN MONONUCLEOTIDE / Chem-LU2 / FMN reductase / Flavin reductase
Function and homology information
Biological speciesFlavonifractor plautii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.25 Å
AuthorsHong, S. / Yang, G.H. / Zhang, P.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31921006, 31630003 China
CitationJournal: Nat Commun / Year: 2021
Title: Discovery of an ene-reductase for initiating flavone and flavonol catabolism in gut bacteria.
Authors: Yang, G. / Hong, S. / Yang, P. / Sun, Y. / Wang, Y. / Zhang, P. / Jiang, W. / Gu, Y.
History
DepositionSep 18, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 3, 2021Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cd1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1763
Polymers34,4341
Non-polymers7432
Water1,856103
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area790 Å2
ΔGint-5 kcal/mol
Surface area16400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.465, 65.465, 193.544
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-568-

HOH

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Components

#1: Protein Cd1 / FMN reductase / Flavodoxin family protein


Mass: 34433.512 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavonifractor plautii (bacteria) / Gene: A4U99_05915, ERS852544_00852, GXM20_05520 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A174NXS8, UniProt: G9YLX2*PLUS
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-LU2 / 2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-4H-chromen-4-one / Luteolin / Luteolin


Mass: 286.236 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H10O6
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 3.01 Å3/Da / Density % sol: 59.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M magnesium formate dihydrate and 15 w/v polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97849 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97849 Å / Relative weight: 1
ReflectionResolution: 2.25→30 Å / Num. obs: 29463 / % possible obs: 100 % / Redundancy: 11.6 % / CC1/2: 0.899 / Net I/σ(I): 24.4
Reflection shellResolution: 2.25→2.33 Å / Num. unique obs: 16462 / CC1/2: 0.899

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2.25→28.023 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2549 2938 9.97 %
Rwork0.1949 26525 -
obs0.2008 29463 77.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 98.28 Å2 / Biso mean: 37.2144 Å2 / Biso min: 10.8 Å2
Refinement stepCycle: final / Resolution: 2.25→28.023 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2224 0 50 103 2377
Biso mean--21.73 39.39 -
Num. residues----288
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092327
X-RAY DIFFRACTIONf_angle_d0.9593146
X-RAY DIFFRACTIONf_chiral_restr0.114332
X-RAY DIFFRACTIONf_plane_restr0.004406
X-RAY DIFFRACTIONf_dihedral_angle_d18.4571366
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.25-2.28680.3533540.287947830
2.2868-2.32620.3228610.231254233
2.3262-2.36850.3449650.251660538
2.3685-2.41410.3187730.245168242
2.4141-2.46330.256850.25676147
2.4633-2.51680.3505890.245680849
2.5168-2.57530.31411010.246489455
2.5753-2.63970.35661140.2455102163
2.6397-2.7110.33151390.2522125876
2.711-2.79070.3221790.2424154896
2.7907-2.88070.25271820.2294163599
2.8807-2.98360.30991780.23041658100
2.9836-3.10290.27311780.21441626100
3.1029-3.24390.22861790.21751614100
3.2439-3.41460.26731790.20131637100
3.4146-3.62810.26261870.18441632100
3.6281-3.90760.24611800.16031626100
3.9076-4.29960.20661790.15081635100
4.2996-4.91880.22751770.14851634100
4.9188-6.18620.20641790.17741620100
6.1862-28.0230.24071800.1959161198
Refinement TLS params.Method: refined / Origin x: -0.3394 Å / Origin y: -15.0461 Å / Origin z: -1.3259 Å
111213212223313233
T0.0498 Å2-0.1423 Å2-0.0369 Å2-0.1692 Å20.0435 Å2--0.1018 Å2
L0.0553 °2-0.0188 °20.0517 °2-0.0454 °2-0.0029 °2--0.0614 °2
S0.0059 Å °0.0608 Å °-0.0079 Å °0.0677 Å °-0.0219 Å °-0.0435 Å °0.0133 Å °0.1687 Å °0.0129 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 308
2X-RAY DIFFRACTION1allA309
3X-RAY DIFFRACTION1allA400
4X-RAY DIFFRACTION1allZ6 - 14
5X-RAY DIFFRACTION1allS1 - 103

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