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- PDB-7d38: flavone reductase -

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Basic information

Entry
Database: PDB / ID: 7d38
Titleflavone reductase
ComponentsCd1
KeywordsFLAVOPROTEIN / flavone reductase / FMN
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
chrysin / FLAVIN MONONUCLEOTIDE / FMN reductase / Flavin reductase
Similarity search - Component
Biological speciesFlavonifractor plautii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.649 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 1.1Oct 23, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_residues
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)35,1443
Polymers34,4341
Non-polymers7112
Water57632
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area950 Å2
ΔGint-10 kcal/mol
Surface area16380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.365, 66.365, 194.057
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-57D / chrysin / 5,7-dihydroxy-2-phenyl-4H-chromen-4-one


Mass: 254.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H10O4 / Feature type: SUBJECT OF INVESTIGATION
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 3.1 Å3/Da / Density % sol: 60.36 %
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: 0.9785 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: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.649→30 Å / Num. obs: 20566 / % possible obs: 99.7 % / Redundancy: 21.8 % / CC1/2: 0.998 / Net I/σ(I): 30
Reflection shellResolution: 2.65→2.74 Å / Num. unique obs: 11637 / CC1/2: 0.973

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.649→29.908 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2478 2077 10.1 %
Rwork0.1903 18489 -
obs0.1961 20566 85.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 114.22 Å2 / Biso mean: 41.1069 Å2 / Biso min: 11.84 Å2
Refinement stepCycle: final / Resolution: 2.649→29.908 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2224 0 50 32 2306
Biso mean--21.73 39.31 -
Num. residues----288
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092325
X-RAY DIFFRACTIONf_angle_d1.0133142
X-RAY DIFFRACTIONf_chiral_restr0.118332
X-RAY DIFFRACTIONf_plane_restr0.005406
X-RAY DIFFRACTIONf_dihedral_angle_d18.3491366
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.6494-2.7110.327620.257356340
2.711-2.77880.271810.252367446
2.7788-2.85390.3247860.259779755
2.8539-2.93780.33171030.23493865
2.9378-3.03250.32331350.2584118581
3.0325-3.14080.30491520.2425140697
3.1408-3.26640.27421580.21961406100
3.2664-3.41480.30931630.20891435100
3.4148-3.59460.25691600.18821460100
3.5946-3.81940.23771640.17171431100
3.8194-4.11360.21261610.15381453100
4.1136-4.52630.21881650.14441426100
4.5263-5.17830.18471610.16271438100
5.1783-6.5130.23921640.19091441100
6.513-29.9080.23241620.20111436100
Refinement TLS params.Method: refined / Origin x: -0.6686 Å / Origin y: -15.4418 Å / Origin z: -1.1928 Å
111213212223313233
T0.108 Å2-0.1008 Å2-0.0304 Å2-0.226 Å20.0269 Å2--0.1815 Å2
L0.1691 °2-0.0747 °20.1592 °2-0.2456 °20.0542 °2--0.4104 °2
S-0.0169 Å °0.074 Å °0.0309 Å °0.1071 Å °-0.0407 Å °-0.0652 Å °-0.0116 Å °0.2793 Å °-0.0481 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 310
2X-RAY DIFFRACTION1allS1 - 32

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