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- PDB-8rdl: Xenorhabdin methyltransferase XrdM with SAH -

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Basic information

Entry
Database: PDB / ID: 8rdl
TitleXenorhabdin methyltransferase XrdM with SAH
ComponentsToxA protein
KeywordsTRANSFERASE / Methyltransferase / dithiopyrrolone / natural product / xenorabdin
Function / homologyMethyltransferase domain 25 / Methyltransferase domain / S-adenosyl-L-methionine-dependent methyltransferase superfamily / S-ADENOSYL-L-HOMOCYSTEINE / ToxA protein
Function and homology information
Biological speciesXenorhabdus doucetiae FRM16 = DSM 17909 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsHuber, E.M. / Groll, M.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)SFB1309-325871075 Germany
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2024
Title: Isofunctional but Structurally Different Methyltransferases for Dithiolopyrrolone Diversification.
Authors: Su, L. / Huber, E.M. / Westphalen, M. / Gellner, J. / Bode, E. / Kobel, T. / Grun, P. / Alanjary, M.M. / Glatter, T. / Cirnski, K. / Muller, R. / Schindler, D. / Groll, M. / Bode, H.B.
History
DepositionDec 8, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 16, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ToxA protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4812
Polymers28,0971
Non-polymers3841
Water39622
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, The assembly in the crystal lattice is artificial. The enzyme does not form a homodimer in solution.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10740 Å2
Unit cell
Length a, b, c (Å)72.500, 72.500, 104.960
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein ToxA protein / XrdM


Mass: 28096.875 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenorhabdus doucetiae FRM16 = DSM 17909 (bacteria)
Gene: XDD1_1316 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold / References: UniProt: A0A068QT41
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.45 Å3/Da / Density % sol: 49.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 9 / Details: 0.1 M Bicine pH 9.0, 30 % PEG6000

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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 PILATUS 6M-F / Detector: PIXEL / Date: Aug 24, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→46 Å / Num. obs: 16946 / % possible obs: 99.6 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.041 / Net I/σ(I): 18.6
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.697 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2156 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→30 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.956 / SU B: 13.783 / SU ML: 0.152 / Cross valid method: THROUGHOUT / ESU R: 0.538 / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2289 845 5 %RANDOM
Rwork0.20016 ---
obs0.20161 16059 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 62.081 Å2
Baniso -1Baniso -2Baniso -3
1--0.76 Å2-0 Å20 Å2
2---0.76 Å20 Å2
3---1.53 Å2
Refinement stepCycle: 1 / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1619 0 26 22 1667
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0131689
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161564
X-RAY DIFFRACTIONr_angle_refined_deg1.1681.6372288
X-RAY DIFFRACTIONr_angle_other_deg1.1161.5773601
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3265204
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.01722.56182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.75915272
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.421157
X-RAY DIFFRACTIONr_chiral_restr0.0430.2216
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021909
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02392
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_it3.1624.943825
X-RAY DIFFRACTIONr_mcbond_other3.164.942825
X-RAY DIFFRACTIONr_mcangle_it4.5287.4031026
X-RAY DIFFRACTIONr_mcangle_other4.5287.4051027
X-RAY DIFFRACTIONr_scbond_it3.1275.317864
X-RAY DIFFRACTIONr_scbond_other3.1265.317864
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.0587.8421263
X-RAY DIFFRACTIONr_long_range_B_refined5.67856.7711785
X-RAY DIFFRACTIONr_long_range_B_other5.67856.7531785
X-RAY DIFFRACTIONr_rigid_bond_restr0.78133251
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 61 -
Rwork0.285 1148 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 11.8034 Å / Origin y: -5.6772 Å / Origin z: -10.188 Å
111213212223313233
T0.1801 Å20.0428 Å20.045 Å2-0.0629 Å20.0098 Å2--0.0426 Å2
L1.0865 °20.5465 °2-0.7258 °2-2.3117 °2-0.2006 °2--1.4491 °2
S0.103 Å °-0.0096 Å °0.0155 Å °0.0582 Å °-0.0189 Å °-0.1349 Å °-0.0431 Å °-0.1741 Å °-0.0841 Å °

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