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- PDB-5oe5: Crystal structure of the N-terminal domain of PqsA in complex wit... -

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Basic information

Entry
Database: PDB / ID: 5oe5
TitleCrystal structure of the N-terminal domain of PqsA in complex with anthraniloyl-AMP (crystal form 3)
ComponentsAnthranilate--CoA ligase
KeywordsLIGASE / PQS / PqsA / Anthranilate / Anthraniloyl-AMP / Anthraniloyl-CoA / Pseudomonas Quinolone Signal / Pseudomonas aeruginosa / Quorum Sensing / Aryl-CoA ligase / ANL superfamily
Function / homology
Function and homology information


anthranilate-CoA ligase / anthranilate-CoA ligase activity / acid-thiol ligase activity / secondary metabolite biosynthetic process / ATP binding
Similarity search - Function
ANL, N-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / AMP-dependent synthetase/ligase / AMP-binding enzyme / AMP-binding enzyme, C-terminal domain superfamily
Similarity search - Domain/homology
Chem-3UK / DI(HYDROXYETHYL)ETHER / Anthranilate--CoA ligase
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.74 Å
AuthorsWitzgall, F. / Ewert, W. / Blankenfeldt, W.
CitationJournal: Chembiochem / Year: 2017
Title: Structures of the N-Terminal Domain of PqsA in Complex with Anthraniloyl- and 6-Fluoroanthraniloyl-AMP: Substrate Activation in Pseudomonas Quinolone Signal (PQS) Biosynthesis.
Authors: Witzgall, F. / Ewert, W. / Blankenfeldt, W.
History
DepositionJul 7, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 6, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Anthranilate--CoA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0744
Polymers44,3951
Non-polymers6793
Water5,927329
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.700, 84.204, 64.237
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Anthranilate--CoA ligase


Mass: 44395.195 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: pqsA, PA0996 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9I4X3, anthranilate-CoA ligase
#2: Chemical ChemComp-3UK / 5'-O-[(S)-[(2-aminobenzoyl)oxy](hydroxy)phosphoryl]adenosine


Mass: 466.342 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H19N6O8P
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


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


Mass: 18.015 Da / Num. of mol.: 329 / Source method: isolated from a natural source / Formula: H2O

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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: 2.12 Å3/Da / Density % sol: 42.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.3
Details: 100 mM tri-sodium citrate (pH 6.3), 240 mM ammonium acetate, 28.5% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.74→47.24 Å / Num. obs: 39169 / % possible obs: 99.3 % / Redundancy: 12.6 % / Biso Wilson estimate: 18.34 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.185 / Rpim(I) all: 0.054 / Rrim(I) all: 0.193 / Net I/σ(I): 10.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) all% possible all
1.74-1.7712.41.3710.6170.4031.4398.7
9.04-47.24110.0720.9980.0220.07699.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.5.31data scaling
PHASERphasing
PHENIX1.12rc2_2821refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
Coot0.8.8model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.74→47.236 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.43
RfactorNum. reflection% reflection
Rfree0.2768 1885 4.82 %
Rwork0.2279 --
obs0.2302 39133 99.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 88.88 Å2 / Biso mean: 27.252 Å2 / Biso min: 7.23 Å2
Refinement stepCycle: final / Resolution: 1.74→47.236 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2994 0 85 329 3408
Biso mean--24.82 29.05 -
Num. residues----390
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023228
X-RAY DIFFRACTIONf_angle_d0.4894400
X-RAY DIFFRACTIONf_chiral_restr0.038474
X-RAY DIFFRACTIONf_plane_restr0.003603
X-RAY DIFFRACTIONf_dihedral_angle_d15.1851949
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7401-1.78710.40471500.34442796294698
1.7871-1.83970.36611470.34682755290298
1.8397-1.89910.35371500.32062811296199
1.8991-1.9670.34331430.30242800294398
1.967-2.04580.2971610.29092821298299
2.0458-2.13890.31581590.26452815297499
2.1389-2.25160.31081090.25862889299899
2.2516-2.39270.2911570.2492841299899
2.3927-2.57740.28351310.23772881301299
2.5774-2.83680.31791520.235228613013100
2.8368-3.24720.28711540.209729233077100
3.2472-4.09070.20951430.172429473090100
4.0907-47.25320.19251290.172931083237100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.82320.08840.03481.5145-0.05730.9474-0.0111-0.08840.0408-0.00920.0243-0.0828-0.20490.1733-0.00750.1768-0.02390.01040.1347-0.03760.18333.489118.8582-6.4466
22.6711-0.79170.6243.3683-0.18181.86370.10110.08370.0305-0.2676-0.0183-0.06030.052-0.0367-0.09240.0886-0.01130.010.072-0.04050.1323-7.234913.3694-18.0217
31.8327-0.0221-0.3471.31420.08281.17090.07080.1960.1644-0.06640.0697-0.0142-0.1457-0.13320.00750.14630.02580.02650.12320.03860.1324-18.922923.0584-18.5857
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 155 )A2 - 155
2X-RAY DIFFRACTION2chain 'A' and (resid 156 through 189 )A156 - 189
3X-RAY DIFFRACTION3chain 'A' and (resid 190 through 399 )A190 - 399

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