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- PDB-8rye: AzeJ in complex with MTA and AZE from Pseudomonas aeruginosa (P2(... -

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Basic information

Entry
Database: PDB / ID: 8rye
TitleAzeJ in complex with MTA and AZE from Pseudomonas aeruginosa (P2(1)2(1)2)
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 / 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
C: Class I SAM-dependent methyltransferase
D: Class I SAM-dependent methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,83923
Polymers110,2574
Non-polymers2,58219
Water4,486249
1
A: Class I SAM-dependent methyltransferase
B: Class I SAM-dependent methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,53013
Polymers55,1282
Non-polymers1,40111
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5560 Å2
ΔGint-90 kcal/mol
Surface area18830 Å2
MethodPISA
2
C: Class I SAM-dependent methyltransferase
hetero molecules

D: Class I SAM-dependent methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,30910
Polymers55,1282
Non-polymers1,1818
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area4970 Å2
ΔGint-85 kcal/mol
Surface area18070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.640, 82.150, 94.670
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Class I SAM-dependent methyltransferase


Mass: 27564.158 Da / Num. of mol.: 4
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 , 5 types, 268 molecules

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


Mass: 297.334 Da / Num. of mol.: 4 / 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.: 4 / Source method: obtained synthetically / Formula: C4H7NO2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 249 / 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: 2.52 Å3/Da / Density % sol: 51.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1 M HEPES, 2.4 M (NH4)2SO4

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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: Mar 25, 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: 80170 / % possible obs: 98.1 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 16.3
Reflection shellResolution: 1.95→2.05 Å / Rmerge(I) obs: 0.688 / Num. unique obs: 11096 / % possible all: 98.7

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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: 0.966 / Cor.coef. Fo:Fc free: 0.949 / SU B: 7.736 / SU ML: 0.096 / Cross valid method: THROUGHOUT / ESU R: 0.372 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20921 4008 5 %RANDOM
Rwork0.164 ---
obs0.16625 76143 98.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.695 Å2
Baniso -1Baniso -2Baniso -3
1--1.3 Å20 Å2-0 Å2
2--0.44 Å20 Å2
3---0.85 Å2
Refinement stepCycle: 1 / Resolution: 1.95→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7344 0 161 249 7754
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0137646
X-RAY DIFFRACTIONr_bond_other_d0.0010.0147155
X-RAY DIFFRACTIONr_angle_refined_deg1.2271.64810347
X-RAY DIFFRACTIONr_angle_other_deg1.2071.58516331
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7845936
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.13819.426470
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.6151243
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.63815100
X-RAY DIFFRACTIONr_chiral_restr0.0490.2966
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.028646
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021914
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_it2.1883.4693756
X-RAY DIFFRACTIONr_mcbond_other2.1853.4683755
X-RAY DIFFRACTIONr_mcangle_it3.0455.2014688
X-RAY DIFFRACTIONr_mcangle_other3.0465.2024689
X-RAY DIFFRACTIONr_scbond_it2.5633.9643889
X-RAY DIFFRACTIONr_scbond_other2.5633.9653890
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.3555.795652
X-RAY DIFFRACTIONr_long_range_B_refined4.28441.0458212
X-RAY DIFFRACTIONr_long_range_B_other4.24340.9518167
X-RAY DIFFRACTIONr_rigid_bond_restr0.749314799
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
Rfree0.325 294 -
Rwork0.234 5585 -
obs--98.82 %
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)
10.0803-0.0589-0.05680.07250.06150.1160.00530.00630.00280.00450.0002-0.0004-0.01120.0014-0.00560.0430.0020.00180.0401-0.00130.0049-16.44217.194-28.732
20.06450.0288-0.00740.1796-0.08150.0787-0.0057-0.0015-0.0019-0.0076-0.0028-0.0161-0.00250.00060.00850.0407-0.0018-0.00460.0371-0.00020.0049.01720.872-17.09
30.18240.08220.13430.08310.08980.1831-0.0017-0.02890.0188-0.0054-0.0189-0.0034-0.0015-0.01760.02050.0331-0.0064-0.00110.0521-0.00190.008316.25416.07518.996
40.14880.07490.11230.11190.08470.23740.00210.01970.0220.01330.00170.0119-0.00310.0134-0.00380.03110.0052-0.00130.0476-0.0030.0071-21.4238.50830.412
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 245
2X-RAY DIFFRACTION1A301
3X-RAY DIFFRACTION2B13 - 245
4X-RAY DIFFRACTION2B301
5X-RAY DIFFRACTION3C13 - 245
6X-RAY DIFFRACTION3C301
7X-RAY DIFFRACTION4D13 - 245
8X-RAY DIFFRACTION4D301

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