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- PDB-6u0s: Crystal structure of the flavin-dependent monooxygenase PieE in c... -

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Basic information

Entry
Database: PDB / ID: 6u0s
TitleCrystal structure of the flavin-dependent monooxygenase PieE in complex with FAD and substrate
Components2,4-dichlorophenol 6-monooxygenase
KeywordsFLAVOPROTEIN / flavin-dependent monooxygenase
Function / homology
Function and homology information


oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen / FAD binding
Similarity search - Function
Glutaredoxin - #120 / Aromatic-ring hydroxylase, C-terminal / : / FAD-binding domain / FAD binding domain / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Glutaredoxin ...Glutaredoxin - #120 / Aromatic-ring hydroxylase, C-terminal / : / FAD-binding domain / FAD binding domain / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Glutaredoxin / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / TRIETHYLENE GLYCOL / Chem-PKS / 2,4-dichlorophenol 6-monooxygenase
Similarity search - Component
Biological speciesStreptomyces sp. SCSIO 03032 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.52 Å
AuthorsShi, R. / Manenda, M.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)436202 Canada
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Structural analyses of the Group A flavin-dependent monooxygenase PieE reveal a sliding FAD cofactor conformation bridging OUT and IN conformations.
Authors: Manenda, M.S. / Picard, M.E. / Zhang, L. / Cyr, N. / Zhu, X. / Barma, J. / Pascal, J.M. / Couture, M. / Zhang, C. / Shi, R.
History
DepositionAug 14, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 15, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 2,4-dichlorophenol 6-monooxygenase
B: 2,4-dichlorophenol 6-monooxygenase
C: 2,4-dichlorophenol 6-monooxygenase
D: 2,4-dichlorophenol 6-monooxygenase
E: 2,4-dichlorophenol 6-monooxygenase
F: 2,4-dichlorophenol 6-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)398,52645
Polymers388,5276
Non-polymers9,99939
Water12,611700
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.339, 187.129, 239.089
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
2,4-dichlorophenol 6-monooxygenase / PieE


Mass: 64754.434 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. SCSIO 03032 (bacteria)
Gene: CAG99_26330 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: W0C4C9

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Non-polymers , 7 types, 739 molecules

#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-PKS / 2-[(2E,5E,7E,9R,10R,11E)-10-hydroxy-3,7,9,11-tetramethyltrideca-2,5,7,11-tetraen-1-yl]-6-methoxy-3-methylpyridin-4-ol


Mass: 385.540 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C24H35NO3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#7: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 700 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.64 Å3/Da / Density % sol: 53.43 % / Mosaicity: 0.36 °
Crystal growTemperature: 295 K / Method: microbatch / pH: 7.5 / Details: 30% PEG 400, 0.2M MgCl2, and 0.1 HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Dec 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.52→49.12 Å / Num. obs: 138900 / % possible obs: 100 % / Redundancy: 7 % / CC1/2: 0.996 / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.053 / Rrim(I) all: 0.141 / Net I/σ(I): 11.1 / Num. measured all: 967629 / Scaling rejects: 466
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.52-2.566.81.3374644867870.4890.5511.4472100
13.8-49.126.10.05558139590.9960.0240.06123.397.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
SCALA0.5.23data scaling
PDB_EXTRACT3.25data extraction
MOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6U0P

6u0p


Resolution: 2.52→49.12 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.924 / WRfactor Rfree: 0.2321 / WRfactor Rwork: 0.1801 / FOM work R set: 0.8136 / SU B: 10.569 / SU ML: 0.226 / SU R Cruickshank DPI: 0.5617 / SU Rfree: 0.2824 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.562 / ESU R Free: 0.282 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2395 6860 4.9 %RANDOM
Rwork0.1867 ---
obs0.1893 131942 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 155.22 Å2 / Biso mean: 55.781 Å2 / Biso min: 18.02 Å2
Baniso -1Baniso -2Baniso -3
1--0.42 Å20 Å2-0 Å2
2--0.62 Å2-0 Å2
3----0.2 Å2
Refinement stepCycle: final / Resolution: 2.52→49.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26549 0 669 700 27918
Biso mean--69.01 41.8 -
Num. residues----3476
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01227904
X-RAY DIFFRACTIONr_angle_refined_deg1.4731.6738079
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.96453470
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.38319.851602
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.077153956
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.91315312
X-RAY DIFFRACTIONr_chiral_restr0.1030.23477
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0222270
LS refinement shellResolution: 2.52→2.585 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 460 -
Rwork0.297 9660 -
all-10120 -
obs--99.99 %

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