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- PDB-7d3a: flavone reductase -

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Basic information

Entry
Database: PDB / ID: 7d3a
Titleflavone reductase
ComponentsCd1
KeywordsFLAVOPROTEIN / flavone reductase / FMN / apigenin
Function / homology
Function and homology information


4 iron, 4 sulfur cluster binding / oxidoreductase activity / nucleotide binding
Similarity search - Function
: / NADPH-dependent FMN reductase-like / NADPH-dependent FMN reductase / Flavoprotein-like superfamily
Similarity search - Domain/homology
Chem-AGI / FLAVIN MONONUCLEOTIDE / FMN reductase / Flavin reductase
Similarity search - Component
Biological speciesFlavonifractor plautii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.552 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
Revision 1.1Sep 29, 2021Group: Advisory / Database references / Category: database_2 / pdbx_unobs_or_zero_occ_residues
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 9, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cd1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1603
Polymers34,4341
Non-polymers7272
Water66737
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1090 Å2
ΔGint-15 kcal/mol
Surface area16380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.969, 63.969, 192.262
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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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
Details: SF file contains Friedel pairs. / 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


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


Mass: 270.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H10O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.86 Å3/Da / Density % sol: 56.93 %
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: 2.55→30 Å / Num. obs: 22019 / % possible obs: 99.9 % / Redundancy: 23.1 % / CC1/2: 0.887 / Net I/σ(I): 28.67
Reflection shellResolution: 2.59→2.64 Å / Num. unique obs: 12318 / CC1/2: 0.887

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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: 2.552→28.618 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2579 2191 9.95 %
Rwork0.1942 19828 -
obs0.2005 22019 88.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 110.48 Å2 / Biso mean: 38.3258 Å2 / Biso min: 10.68 Å2
Refinement stepCycle: final / Resolution: 2.552→28.618 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2224 0 50 37 2311
Biso mean--21.73 34.66 -
Num. residues----288
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092326
X-RAY DIFFRACTIONf_angle_d0.9763144
X-RAY DIFFRACTIONf_chiral_restr0.053332
X-RAY DIFFRACTIONf_plane_restr0.004406
X-RAY DIFFRACTIONf_dihedral_angle_d17.891366
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5521-2.60750.3354670.251762245
2.6075-2.66810.2816800.249170250
2.6681-2.73480.3543940.246582760
2.7348-2.80870.35131170.2611103074
2.8087-2.89130.34931460.2579134296
2.8913-2.98450.32981470.25531371100
2.9845-3.09110.34051560.23611387100
3.0911-3.21470.28351500.20521413100
3.2147-3.36070.27491510.20481397100
3.3607-3.53760.23441600.20151382100
3.5376-3.75880.29611610.18221416100
3.7588-4.04830.24321530.17711375100
4.0483-4.45430.2231550.14371366100
4.4543-5.09570.20231550.1521404100
5.0957-6.40820.24171550.18021410100
6.4082-28.6180.19161440.1967138499
Refinement TLS params.Method: refined / Origin x: 31.3098 Å / Origin y: -18.0378 Å / Origin z: -1.7779 Å
111213212223313233
T0.1055 Å2-0.086 Å20.0216 Å2-0.173 Å2-0.0259 Å2--0.152 Å2
L0.3057 °2-0.1758 °2-0.2541 °2-0.3273 °2-0.0002 °2--0.3901 °2
S0.0527 Å °0.0431 Å °0.0064 Å °0.0201 Å °-0.0163 Å °0.0593 Å °-0.0482 Å °-0.2066 Å °-0.0162 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 308
2X-RAY DIFFRACTION1allA309
3X-RAY DIFFRACTION1allA311
4X-RAY DIFFRACTION1allZ6 - 14
5X-RAY DIFFRACTION1allS1 - 37

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