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- PDB-8ryd: AzeJ in complex with SAH from Pseudomonas aeruginosa -

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Basic information

Entry
Database: PDB / ID: 8ryd
TitleAzeJ in complex with SAH from Pseudomonas aeruginosa
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 / S-ADENOSYL-L-HOMOCYSTEINE / Class I SAM-dependent methyltransferase
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 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)111,7948
Polymers110,2574
Non-polymers1,5384
Water25214
1
A: Class I SAM-dependent methyltransferase
B: Class I SAM-dependent methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,8974
Polymers55,1282
Non-polymers7692
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3060 Å2
ΔGint-17 kcal/mol
Surface area17980 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)55,8974
Polymers55,1282
Non-polymers7692
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area2960 Å2
ΔGint-17 kcal/mol
Surface area18120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.500, 84.150, 94.340
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#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 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9HYR0
#2: Chemical
ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Mass: 384.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O
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: 2.55 Å3/Da / Density % sol: 51.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.9 / Details: 1.8 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: Mar 25, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. obs: 21945 / % possible obs: 94.3 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 14.6
Reflection shellResolution: 3→3.1 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.663 / Num. unique obs: 2080 / % possible all: 97.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→30 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.905 / SU B: 37.974 / SU ML: 0.305 / Cross valid method: THROUGHOUT / ESU R Free: 0.443 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24159 1095 5 %RANDOM
Rwork0.1925 ---
obs0.1949 20801 94.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 71.013 Å2
Baniso -1Baniso -2Baniso -3
1-3.36 Å20 Å20 Å2
2---0.23 Å20 Å2
3----3.12 Å2
Refinement stepCycle: 1 / Resolution: 3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7108 0 104 14 7226
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0010.0137334
X-RAY DIFFRACTIONr_bond_other_d0.0010.0146923
X-RAY DIFFRACTIONr_angle_refined_deg1.1681.6459929
X-RAY DIFFRACTIONr_angle_other_deg1.0321.57715803
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2275906
X-RAY DIFFRACTIONr_dihedral_angle_2_deg23.82119.378450
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.613151201
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5241596
X-RAY DIFFRACTIONr_chiral_restr0.0290.2937
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.028372
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021848
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_it1.196.0463648
X-RAY DIFFRACTIONr_mcbond_other1.196.0463648
X-RAY DIFFRACTIONr_mcangle_it1.7999.0664546
X-RAY DIFFRACTIONr_mcangle_other1.7999.0664547
X-RAY DIFFRACTIONr_scbond_it1.0576.2433686
X-RAY DIFFRACTIONr_scbond_other1.0576.2433686
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.5579.295384
X-RAY DIFFRACTIONr_long_range_B_refined2.63768.9937602
X-RAY DIFFRACTIONr_long_range_B_other2.63768.9967603
X-RAY DIFFRACTIONr_rigid_bond_restr0.19314255
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.077 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 81 -
Rwork0.283 1538 -
obs--96.95 %
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)
11.6785-0.4740.09121.68190.14341.3728-0.0526-0.0485-0.0547-0.0708-0.00020.1151-0.1581-0.1590.05280.11260.1163-0.03590.128-0.01560.0948-17.1615.48-28.107
21.52270.216-0.10532.38450.06791.21720.1424-0.0949-0.0395-0.2106-0.1675-0.1417-0.2648-0.06110.02510.16770.02020.01650.02060.01830.0592721.576-16.811
31.8830.15280.4462.02050.23390.9381-0.0962-0.05110.0913-0.10410.01880.0043-0.17640.12330.07740.1796-0.1654-0.0070.1654-0.00030.02613.97617.91519.301
41.75740.14660.68091.73430.45251.8135-0.12250.0210.19150.02120.05690.09590.0158-0.15670.06570.0279-0.0376-0.03330.14690.02870.0541-22.5295.49130.453
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A16 - 240
2X-RAY DIFFRACTION2B16 - 245
3X-RAY DIFFRACTION3C16 - 245
4X-RAY DIFFRACTION4D15 - 239

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