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- PDB-9ch2: Structure of the alpha-N-methyltransferase (SonM) and RiPP precur... -

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Basic information

Entry
Database: PDB / ID: 9ch2
TitleStructure of the alpha-N-methyltransferase (SonM) and RiPP precursor (SonA-L63D) heteromeric complex
Components
  • (TP-methylase family ...) x 2
  • Extradiol ring-cleavage dioxygenase LigAB LigA subunit domain-containing protein
KeywordsTRANSFERASE / Alpha-N-methyltransferase
Function / homology
Function and homology information


methyltransferase activity / metal ion binding
Similarity search - Function
Dioxygenase LigAB, LigA subunit superfamily / Tetrapyrrole methylase / Tetrapyrrole (Corrin/Porphyrin) Methylases / Tetrapyrrole methylase, subdomain 1 / Tetrapyrrole methylase superfamily
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / Uncharacterized protein / TP-methylase family protein
Similarity search - Component
Biological speciesShewanella oneidensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsCrone, K.K. / Labonte, J.W. / Elias, M. / Freeman, M.F.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM133475 United States
CitationJournal: Protein Sci. / Year: 2025
Title: alpha-N-Methyltransferase regiospecificity is mediated by proximal, redundant enzyme-substrate interactions.
Authors: Crone, K.K. / Labonte, J.W. / Elias, M.H. / Freeman, M.F.
History
DepositionJul 1, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TP-methylase family protein
B: Extradiol ring-cleavage dioxygenase LigAB LigA subunit domain-containing protein
C: TP-methylase family protein
D: Extradiol ring-cleavage dioxygenase LigAB LigA subunit domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,0436
Polymers75,5934
Non-polymers4502
Water2,288127
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9180 Å2
ΔGint-96 kcal/mol
Surface area24550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.270, 92.270, 162.350
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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TP-methylase family ... , 2 types, 2 molecules AC

#1: Protein TP-methylase family protein


Mass: 28955.170 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella oneidensis (bacteria) / Gene: SO_1478 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8EGW3
#3: Protein TP-methylase family protein


Mass: 29068.326 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella oneidensis (bacteria) / Gene: SO_1478 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8EGW3

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Protein , 1 types, 2 molecules BD

#2: Protein Extradiol ring-cleavage dioxygenase LigAB LigA subunit domain-containing protein


Mass: 8784.607 Da / Num. of mol.: 2 / Mutation: L63D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella oneidensis (bacteria) / Gene: SO_1479 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8EGW2

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Non-polymers , 3 types, 129 molecules

#4: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Mass: 384.411 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C14H20N6O5S / Source: (gene. exp.) Shewanella oneidensis (bacteria) / Gene: SO_1478 / Production host: Escherichia coli (E. coli) / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 2.62 Å3/Da / Density % sol: 53.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 240 mM sodium malonate pH 5.5 with 8% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033167 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 16, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033167 Å / Relative weight: 1
ReflectionResolution: 2.35→19.83 Å / Num. obs: 33473 / % possible obs: 98.4 % / Redundancy: 12.05 % / CC1/2: 1 / Rrim(I) all: 0.069 / Net I/σ(I): 36.32
Reflection shellResolution: 2.35→2.45 Å / Num. unique obs: 3932 / CC1/2: 0.703 / Rrim(I) all: 1.339

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→19.83 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.935 / SU B: 15.568 / SU ML: 0.178 / Cross valid method: THROUGHOUT / ESU R: 0.297 / ESU R Free: 0.229 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24013 1674 5 %RANDOM
Rwork0.19007 ---
obs0.19263 31799 98.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 81.939 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20.06 Å20 Å2
2--0.12 Å2-0 Å2
3----0.37 Å2
Refinement stepCycle: 1 / Resolution: 2.35→19.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4811 0 1 127 4939
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0010.0124985
X-RAY DIFFRACTIONr_bond_other_d00.0164706
X-RAY DIFFRACTIONr_angle_refined_deg0.5651.816788
X-RAY DIFFRACTIONr_angle_other_deg0.1881.74110848
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9025623
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.096520
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.09410824
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0250.2763
X-RAY DIFFRACTIONr_gen_planes_refined0.0010.025861
X-RAY DIFFRACTIONr_gen_planes_other00.021116
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_it5.9896.8292480
X-RAY DIFFRACTIONr_mcbond_other5.9786.832480
X-RAY DIFFRACTIONr_mcangle_it7.36812.2533098
X-RAY DIFFRACTIONr_mcangle_other7.3712.2543099
X-RAY DIFFRACTIONr_scbond_it8.3837.582505
X-RAY DIFFRACTIONr_scbond_other8.3817.5822506
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other11.46113.5863688
X-RAY DIFFRACTIONr_long_range_B_refined13.02668.135660
X-RAY DIFFRACTIONr_long_range_B_other13.03568.145648
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.35→2.41 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 121 -
Rwork0.257 2308 -
obs--100 %
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)
10.8098-0.0459-0.1950.9433-0.07970.71690.01330.0094-0.0319-0.06580.0031-0.17590.03630.145-0.01640.0270.00570.00240.0345-0.01180.043655.2243-20.176-11.8755
26.4956-1.2912-2.36384.9411.23925.45970.1276-0.09680.37430.07920.063-0.922-0.20980.581-0.19060.0696-0.0408-0.08310.07250.01830.257369.6517-5.69287.2525
30.59750.1380.40340.75110.36231.2316-0.0419-0.04220.0307-0.010.01680.1145-0.0562-0.09620.02510.0348-0.0095-0.01120.01820.010.02338.9439-10.2151-9.827
44.88630.6303-0.52.93750.90374.85190.0718-0.24630.2720.0011-0.07630.2868-0.2554-0.40060.00450.1164-0.02650.00470.076-0.00820.041129.9946-21.825613.6119
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 301
2X-RAY DIFFRACTION2B10 - 61
3X-RAY DIFFRACTION3C2 - 262
4X-RAY DIFFRACTION4D11 - 61

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