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- PDB-6sw2: Crystal Structure of P. aeruginosa PqsL in complex with 2-aminobe... -

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Basic information

Entry
Database: PDB / ID: 6sw2
TitleCrystal Structure of P. aeruginosa PqsL in complex with 2-aminobenzoylacetate
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
3-(2-aminophenyl)-3-oxopropanoic acid / FLAVIN-ADENINE DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / PHOSPHATE ION / Probable FAD-dependent monooxygenase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 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)46,11611
Polymers44,0481
Non-polymers2,06810
Water3,153175
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint12 kcal/mol
Surface area16160 Å2
Unit cell
Length a, b, c (Å)47.079, 63.984, 128.101
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: 44047.973 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)
Gene: pqsL, PA4190 / Production host: Escherichia coli (E. coli) / Strain (production host): LMG194 / References: UniProt: Q9HWJ1

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Non-polymers , 7 types, 185 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / 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-61M / 3-(2-aminophenyl)-3-oxopropanoic acid / 2-aminobenzoylacetate


Mass: 179.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H9NO3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 2.19 Å3/Da / Density % sol: 43.86 %
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: 0.966 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 1.7→45.31 Å / Num. obs: 43115 / % possible obs: 99.3 % / Redundancy: 4.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.037 / Rrim(I) all: 0.085 / Net I/σ(I): 10.1
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
1.7-1.734.81.4191084322740.5110.6931.587199
9-45.274.30.03114643440.9990.0160.03534.297.1

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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: 1.7→45.31 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.769 / SU ML: 0.085 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.101 / ESU R Free: 0.105
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES - REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2174 2143 5 %RANDOM
Rwork0.1731 ---
obs0.1752 40904 99.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 92.86 Å2 / Biso mean: 29.736 Å2 / Biso min: 16.27 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2--0.98 Å2-0 Å2
3----1.01 Å2
Refinement stepCycle: final / Resolution: 1.7→45.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2870 0 135 175 3180
Biso mean--39.95 37.45 -
Num. residues----367
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0143067
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172735
X-RAY DIFFRACTIONr_angle_refined_deg1.5671.7084137
X-RAY DIFFRACTIONr_angle_other_deg0.9911.6856396
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5035369
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.20619.275193
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.22615487
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.491543
X-RAY DIFFRACTIONr_chiral_restr0.0760.2375
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023486
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02551
LS refinement shellResolution: 1.7→1.744 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 134 -
Rwork0.305 2993 -
all-3127 -
obs--98.8 %

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