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- PDB-8ryf: AzeJ in complex with MTA and AZE from Pseudomonas aeruginosa (P4(2)22) -

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Basic information

Entry
Database: PDB / ID: 8ryf
TitleAzeJ in complex with MTA and AZE from Pseudomonas aeruginosa (P4(2)22)
ComponentsClass I SAM-dependent methyltransferase
KeywordsLYASE / Natural Product Biosynthesis / Non-Proteinogenic Amino Acid / Proline-Homologue / SAM-Turnover / Catalysis
Function / homologyS-adenosyl-L-methionine-dependent methyltransferase superfamily / (2S)-azetidine-2-carboxylic acid / 5'-DEOXY-5'-METHYLTHIOADENOSINE / PHOSPHATE ION / Class I SAM-dependent methyltransferase
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsKlaubert, T.J. / Gellner, J. / Bernard, C. / Effert, J. / Lombard, C. / Kaila, V.R.I. / Bode, H.B. / Li, Y. / Groll, M.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)325871075 (SFB 1309) Germany
CitationJournal: Nat Commun / Year: 2025
Title: Molecular basis for azetidine-2-carboxylic acid biosynthesis.
Authors: Klaubert, T.J. / Gellner, J. / Bernard, C. / Effert, J. / Lombard, C. / Kaila, V.R.I. / Bode, H.B. / Li, Y. / Groll, M.
History
DepositionFeb 8, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 1, 2025Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2025Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.year
Revision 1.2Feb 19, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Class I SAM-dependent methyltransferase
B: Class I SAM-dependent methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,36513
Polymers55,1282
Non-polymers1,23711
Water3,945219
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5800 Å2
ΔGint-44 kcal/mol
Surface area17520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.210, 122.210, 87.060
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number93
Space group name H-MP4222

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Class I SAM-dependent methyltransferase


Mass: 27564.158 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: PA3335 / Plasmid: pETDuet / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9HYR0

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Non-polymers , 7 types, 230 molecules

#2: Chemical ChemComp-MTA / 5'-DEOXY-5'-METHYLTHIOADENOSINE


Mass: 297.334 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H15N5O3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-02A / (2S)-azetidine-2-carboxylic acid


Type: L-peptide linking / Mass: 101.104 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H7NO2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#7: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 219 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.95 Å3/Da / Density % sol: 58.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.2 / Details: 0.8 M sodium potassium phosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 26, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→30 Å / Num. obs: 48492 / % possible obs: 99.8 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 17.1
Reflection shellResolution: 1.95→2.05 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.697 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 6637 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→30 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.955 / SU B: 6.699 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.166 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19686 2423 5 %RANDOM
Rwork0.14606 ---
obs0.14857 46038 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.492 Å2
Baniso -1Baniso -2Baniso -3
1-0.4 Å2-0 Å2-0 Å2
2--0.4 Å2-0 Å2
3----0.8 Å2
Refinement stepCycle: 1 / Resolution: 1.95→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3522 0 80 220 3822
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0133652
X-RAY DIFFRACTIONr_bond_other_d0.0010.0143453
X-RAY DIFFRACTIONr_angle_refined_deg1.2541.6464934
X-RAY DIFFRACTIONr_angle_other_deg1.2521.5817879
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9025451
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.97419.505222
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.7815595
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.211547
X-RAY DIFFRACTIONr_chiral_restr0.0560.2464
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024145
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02911
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_it2.2413.0781810
X-RAY DIFFRACTIONr_mcbond_other2.2293.0741808
X-RAY DIFFRACTIONr_mcangle_it2.9944.6192259
X-RAY DIFFRACTIONr_mcangle_other2.9794.6182259
X-RAY DIFFRACTIONr_scbond_it2.7163.5981840
X-RAY DIFFRACTIONr_scbond_other2.6913.5861837
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.3225.1952668
X-RAY DIFFRACTIONr_long_range_B_refined4.08337.4724032
X-RAY DIFFRACTIONr_long_range_B_other3.95837.1973990
X-RAY DIFFRACTIONr_rigid_bond_restr1.01537100
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 175 -
Rwork0.211 3332 -
obs--99.94 %
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)
10.4102-0.19350.15480.3754-0.0230.48140.03560.0302-0.0014-0.0295-0.04440.01450.01260.0540.00880.01040.01550.00380.030.00690.012643.0694.54321.177
20.1750.15180.1510.6066-0.31810.6811-0.0312-0.0319-0.03250.10020.0019-0.0486-0.1841-0.09830.02930.05730.0293-0.01740.0221-0.01020.022932.38621.70539.165
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A14 - 245
2X-RAY DIFFRACTION1A301
3X-RAY DIFFRACTION2B26 - 246

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