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- PDB-7d39: FLR-apo -

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Basic information

Entry
Database: PDB / ID: 7d39
TitleFLR-apo
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
FLAVIN MONONUCLEOTIDE / FMN reductase / Flavin reductase
Similarity search - Component
Biological speciesFlavonifractor plautii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.198 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: 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
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

Downloads & links

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Assembly

Deposited unit
A: Cd1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8902
Polymers34,4341
Non-polymers4561
Water2,900161
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area680 Å2
ΔGint-5 kcal/mol
Surface area16280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.870, 67.870, 194.270
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
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 3.25 Å3/Da / Density % sol: 62.14 %
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: Apr 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.198→30 Å / Num. obs: 21222 / % possible obs: 99.6 % / Redundancy: 22 % / CC1/2: 0.788 / Net I/σ(I): 34.5
Reflection shellResolution: 2.198→2.28 Å / Num. unique obs: 21222 / CC1/2: 0.788

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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: 2.198→24.284 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 21.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2107 1967 9.46 %
Rwork0.1811 18815 -
obs0.184 20782 86.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 97.13 Å2 / Biso mean: 33.2002 Å2 / Biso min: 16.23 Å2
Refinement stepCycle: final / Resolution: 2.198→24.284 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2224 0 50 161 2435
Biso mean--21.73 41.46 -
Num. residues----288
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092304
X-RAY DIFFRACTIONf_angle_d0.8993112
X-RAY DIFFRACTIONf_chiral_restr0.051332
X-RAY DIFFRACTIONf_plane_restr0.005404
X-RAY DIFFRACTIONf_dihedral_angle_d16.5441365
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1983-2.25330.2525680.203565044
2.2533-2.31410.2413780.207576150
2.3141-2.38220.2585910.210888459
2.3822-2.4590.29251220.2211115175
2.459-2.54680.25341470.2106139292
2.5468-2.64870.24181540.1972147397
2.6487-2.7690.23721570.1985149098
2.769-2.91480.2211590.1901152099
2.9148-3.09710.24641630.193154499
3.0971-3.33570.20191590.1792152899
3.3357-3.67030.21341620.17521557100
3.6703-4.1990.19351650.15761576100
4.199-5.28140.1731670.15481605100
5.2814-24.2840.19261750.1906168498
Refinement TLS params.Method: refined / Origin x: -32.6595 Å / Origin y: -17.6333 Å / Origin z: -0.9014 Å
111213212223313233
T0.1829 Å2-0.086 Å20.0253 Å2-0.2924 Å2-0.0109 Å2--0.2602 Å2
L0.6113 °2-0.3612 °2-0.0949 °2-0.7 °20.0628 °2--1.3417 °2
S0.0136 Å °0.0527 Å °-0.0143 Å °0.0451 Å °-0.0482 Å °0.1103 Å °-0.0513 Å °-0.3711 Å °-0.0085 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 308
2X-RAY DIFFRACTION1allA309
3X-RAY DIFFRACTION1allZ6 - 14
4X-RAY DIFFRACTION1allS1 - 161

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