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- PDB-6sw1: Crystal Structure of P. aeruginosa PqsL: R41Y, I43R, G45R, C105G ... -

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Basic information

Entry
Database: PDB / ID: 6sw1
TitleCrystal Structure of P. aeruginosa PqsL: R41Y, I43R, G45R, C105G mutant
ComponentsProbable FAD-dependent monooxygenase
KeywordsANTIBIOTIC / oxidoreductase / photocatalysis / FAD / NAD(P) / biosynthetic pathway
Function / homology
Function and homology information


3-(3-hydroxyphenyl)propionate hydroxylase activity / 3-(3-hydroxy)phenylpropionate catabolic process / FAD binding
Similarity search - Function
: / FAD-binding domain / FAD binding domain / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / Probable FAD-dependent monooxygenase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsMattevi, A. / Rovida, S.
CitationJournal: Nat Commun / Year: 2020
Title: Photoinduced monooxygenation involving NAD(P)H-FAD sequential single-electron transfer.
Authors: Ernst, S. / Rovida, S. / Mattevi, A. / Fetzner, S. / Drees, S.L.
History
DepositionSep 19, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 3, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 2024Group: 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

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Assembly

Deposited unit
A: Probable FAD-dependent monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3216
Polymers44,1361
Non-polymers1,1855
Water2,792155
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2630 Å2
ΔGint-8 kcal/mol
Surface area15580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.533, 65.751, 135.237
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, 1 molecules A

#1: Protein Probable FAD-dependent monooxygenase


Mass: 44136.039 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: pqsL, PA4190 / Production host: Escherichia coli (E. coli) / Strain (production host): LMG194 / References: UniProt: Q9HWJ1

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Non-polymers , 5 types, 160 molecules

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


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / 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: 2.11 Å3/Da / Density % sol: 41.68 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 20,000 (5-10 % w/v), MES buffer pH 6.5.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9677 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.61→45.08 Å / Num. obs: 54463 / % possible obs: 97.8 % / Redundancy: 5.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.02 / Rrim(I) all: 0.049 / Net I/σ(I): 17.3 / Num. measured all: 305904 / Scaling rejects: 10
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
1.61-1.645.90.7431573826900.4640.3350.8172.198.5
8.82-45.083.20.0325401700.9740.0220.03928.437.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.7.1data scaling
PHASERphasing
REFMAC5.8.0230refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2X3N

2x3n


Resolution: 1.8→38.55 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.94 / SU B: 2.558 / SU ML: 0.079 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.125 / ESU R Free: 0.119
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2216 1988 5.1 %RANDOM
Rwork0.1882 ---
obs0.19 36923 96.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 127.41 Å2 / Biso mean: 31.911 Å2 / Biso min: 18.15 Å2
Baniso -1Baniso -2Baniso -3
1--0.39 Å2-0 Å20 Å2
2--0.57 Å2-0 Å2
3----0.18 Å2
Refinement stepCycle: final / Resolution: 1.8→38.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2878 0 74 155 3107
Biso mean--43.38 36.29 -
Num. residues----367
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0143017
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172660
X-RAY DIFFRACTIONr_angle_refined_deg1.6891.6884088
X-RAY DIFFRACTIONr_angle_other_deg1.031.6476219
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9565370
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.46219.184196
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.0415488
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0871544
X-RAY DIFFRACTIONr_chiral_restr0.0850.2373
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023493
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02552
LS refinement shellResolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 156 -
Rwork0.229 2735 -
all-2891 -
obs--99.14 %

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