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- PDB-8s6l: AzeD dehydratase of Pseudomonas aeruginosa -

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Basic information

Entry
Database: PDB / ID: 8s6l
TitleAzeD dehydratase of Pseudomonas aeruginosa
ComponentsPhthiocerol/phthiodiolone dimycocerosyl transferase
KeywordsBIOSYNTHETIC PROTEIN / dehydratase / post-NRPS enzyme / tailoring enzyme / azetidomonamide dehydratase
Function / homology: / phenolphthiocerol/phthiocerol/phthiodiolone dimycocerosyl transferase / Phthiocerol/phthiodiolone dimycocerosyl transferase, C-terminal / Phthiocerol/phthiodiolone dimycocerosyl transferase C-terminus / Condensation domain / Condensation domain / Chloramphenicol acetyltransferase-like domain superfamily / acyltransferase activity / Phthiocerol/phthiodiolone dimycocerosyl transferase
Function and homology information
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsCalderari, A. / Gruez, A. / Najah, S. / Li, Y. / Weissman, K.J.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-20-CE92-0038 France
CitationJournal: To be published
Title: High resolution structure of azetidomonamide dehydratase
Authors: Calderari, A. / Gruez, A. / Najah, S. / Li, Y. / Weissman, K.J.
History
DepositionFeb 27, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 12, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phthiocerol/phthiodiolone dimycocerosyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,4263
Polymers51,2421
Non-polymers1842
Water6,089338
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area560 Å2
ΔGint-2 kcal/mol
Surface area17670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.460, 67.590, 116.680
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Phthiocerol/phthiodiolone dimycocerosyl transferase / Acyltransferase PapA5 / Phthiocerol/phthiodiolone O-acyltransferase / Polyketide synthase- ...Acyltransferase PapA5 / Phthiocerol/phthiodiolone O-acyltransferase / Polyketide synthase-associated protein A5


Mass: 51241.734 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: PA3329 / Plasmid: pET28a / Details (production host): His6 tag / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9HYR6, phenolphthiocerol/phthiocerol/phthiodiolone dimycocerosyl transferase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 338 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.17 Å3/Da / Density % sol: 43.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 100 mM bis-Tris methane at pH 6.5 and 25% PEG-3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.980112 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 12, 2023
RadiationMonochromator: channel-cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.980112 Å / Relative weight: 1
ReflectionResolution: 1.55→44.2 Å / Num. obs: 65281 / % possible obs: 99.9 % / Redundancy: 13.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.019 / Rrim(I) all: 0.067 / Χ2: 0.9 / Net I/σ(I): 20
Reflection shellResolution: 1.55→1.59 Å / % possible obs: 98.7 % / Redundancy: 13.6 % / Rmerge(I) obs: 1.079 / Num. measured all: 63708 / Num. unique obs: 4701 / CC1/2: 0.769 / Rpim(I) all: 0.303 / Rrim(I) all: 1.122 / Χ2: 0.58 / Net I/σ(I) obs: 1.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→44.2 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.959 / SU B: 4.079 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.085 / ESU R Free: 0.076 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19447 3261 5 %RANDOM
Rwork0.14568 ---
obs0.14808 61945 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.346 Å2
Baniso -1Baniso -2Baniso -3
1--3.22 Å20 Å2-0 Å2
2--4.01 Å20 Å2
3----0.78 Å2
Refinement stepCycle: 1 / Resolution: 1.55→44.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3393 0 12 340 3745
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0123546
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163347
X-RAY DIFFRACTIONr_angle_refined_deg1.4671.6564841
X-RAY DIFFRACTIONr_angle_other_deg0.5231.577670
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2545450
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.404550
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.8510548
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0770.2532
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024395
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02869
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7442.4191769
X-RAY DIFFRACTIONr_mcbond_other1.7442.4211770
X-RAY DIFFRACTIONr_mcangle_it2.3234.3582223
X-RAY DIFFRACTIONr_mcangle_other2.3244.362224
X-RAY DIFFRACTIONr_scbond_it1.9692.7841777
X-RAY DIFFRACTIONr_scbond_other1.9682.7841778
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.6494.9482617
X-RAY DIFFRACTIONr_long_range_B_refined3.45425.093849
X-RAY DIFFRACTIONr_long_range_B_other3.27924.253786
X-RAY DIFFRACTIONr_rigid_bond_restr3.77836893
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.552→1.593 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.408 234 -
Rwork0.348 4447 -
obs--98.63 %

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