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

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Basic information

Entry
Database: PDB / ID: 9chi
TitleStructure of the alpha-N-methyltransferase (SonM) and RiPP precursor (SonA-Y62A) heteromeric complex (bound to SAH - structure 2)
Components
  • (SonA) x 2
  • Alpha-N-methyltransferase
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 MR-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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: Alpha-N-methyltransferase
B: SonA
C: Alpha-N-methyltransferase
D: SonA
E: Alpha-N-methyltransferase
F: SonA
G: Alpha-N-methyltransferase
H: SonA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,91712
Polymers145,3798
Non-polymers1,5384
Water5,513306
1
A: Alpha-N-methyltransferase
B: SonA
C: Alpha-N-methyltransferase
D: SonA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,4516
Polymers72,6834
Non-polymers7692
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12830 Å2
ΔGint-77 kcal/mol
Surface area23400 Å2
MethodPISA
2
E: Alpha-N-methyltransferase
F: SonA
G: Alpha-N-methyltransferase
H: SonA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,4656
Polymers72,6974
Non-polymers7692
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12730 Å2
ΔGint-78 kcal/mol
Surface area23360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.050, 59.060, 108.580
Angle α, β, γ (deg.)89.95, 90.11, 85.97
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Alpha-N-methyltransferase / SonM


Mass: 28937.131 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella oneidensis MR-1 (bacteria) / Gene: SO_1478 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8EGW3
#2: Protein SonA


Mass: 7411.169 Da / Num. of mol.: 3 / Mutation: Y62A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella oneidensis MR-1 (bacteria) / Gene: SO_1479 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8EGW2
#3: Protein SonA


Mass: 7397.143 Da / Num. of mol.: 1 / Mutation: Y62A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella oneidensis MR-1 (bacteria) / Gene: SO_1479 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8EGW2
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 306 / 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: 2.18 Å3/Da / Density % sol: 43.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 240 mM sodium malonate pH 6, 12% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 26, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.2→19.64 Å / Num. obs: 56505 / % possible obs: 86.3 % / Redundancy: 2.01 % / CC1/2: 0.995 / Rrim(I) all: 0.09 / Net I/σ(I): 7.15
Reflection shellResolution: 2.2→2.3 Å / Num. unique obs: 7177 / CC1/2: 0.931 / Rrim(I) all: 0.39

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→19.64 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.894 / SU B: 17.493 / SU ML: 0.232 / Cross valid method: THROUGHOUT / ESU R: 0.126 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.3088 2872 5.1 %RANDOM
Rwork0.26469 ---
obs0.26703 53632 85.87 %-
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: 38.435 Å2
Baniso -1Baniso -2Baniso -3
1--13.96 Å216.39 Å29.39 Å2
2--2.7 Å2-0.44 Å2
3---11.26 Å2
Refinement stepCycle: 1 / Resolution: 2.2→19.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10068 0 104 306 10478
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0010.01210477
X-RAY DIFFRACTIONr_bond_other_d00.0169897
X-RAY DIFFRACTIONr_angle_refined_deg0.4481.80914253
X-RAY DIFFRACTIONr_angle_other_deg0.1521.74122795
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.52651303
X-RAY DIFFRACTIONr_dihedral_angle_2_deg1.163544
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.06101713
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0210.21602
X-RAY DIFFRACTIONr_gen_planes_refined0.0010.0212320
X-RAY DIFFRACTIONr_gen_planes_other00.022328
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_it2.6393.0455233
X-RAY DIFFRACTIONr_mcbond_other2.6393.0455232
X-RAY DIFFRACTIONr_mcangle_it3.8585.4546524
X-RAY DIFFRACTIONr_mcangle_other3.8575.4546525
X-RAY DIFFRACTIONr_scbond_it3.073.3835244
X-RAY DIFFRACTIONr_scbond_other3.0693.3835245
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.7616.0627726
X-RAY DIFFRACTIONr_long_range_B_refined6.71832.4812193
X-RAY DIFFRACTIONr_long_range_B_other6.71432.4212170
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.252 Å
RfactorNum. reflection% reflection
Rfree0.378 198 -
Rwork0.328 3641 -
obs--79.58 %
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)
10.2946-0.03590.15020.2366-0.09680.38120.010.02110.0097-0.02680.0049-0.0314-0.0551-0.0383-0.01490.0588-0.02540.04630.0448-0.02920.039814.551-16.012-3.071
21.9985-0.51-0.62650.20460.41051.04430.0983-0.03080.1528-0.0668-0.018-0.0441-0.1852-0.0603-0.08030.081-0.030.05660.0425-0.03820.05350.94-9.93814.518
30.1542-0.0743-0.01380.29840.02130.32150.03380.0272-0.0368-0.0316-0.03320.02070.03940.0351-0.00060.0652-0.03320.03290.0517-0.04440.042911.611-35.227-3.062
41.3307-0.18860.75350.0487-0.06670.71960.12370.0609-0.0960.0027-0.00280.00150.10470.0184-0.12090.105-0.04580.02790.048-0.03710.05325.053-41.35414.51
50.23610.00780.15790.24390.06820.326-0.0015-0.00060.0109-0.03130.0086-0.0039-0.03490.0071-0.00710.0605-0.04160.04330.0302-0.03130.033237.054-23.14251.207
62.312-0.5638-0.92820.27230.2650.8080.0996-0.07570.1378-0.04180.01790.009-0.0950.0138-0.11760.0606-0.04610.0510.0449-0.04090.071323.321-17.15868.917
70.2538-0.0789-0.15530.31790.07240.3595-0.0048-0.021-0.0569-0.025-0.0321-0.00550.01890.00040.03690.0509-0.03880.0430.0444-0.02770.04834.126-42.37251.217
81.788-0.14331.25260.16240.18971.76450.1095-0.0893-0.2273-0.0110.0925-0.02120.1648-0.0477-0.2020.0947-0.04160.0410.1132-0.01860.075647.47-48.61768.696
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 263
2X-RAY DIFFRACTION1A301
3X-RAY DIFFRACTION2B10 - 70
4X-RAY DIFFRACTION3C2 - 263
5X-RAY DIFFRACTION3C301
6X-RAY DIFFRACTION4D11 - 70
7X-RAY DIFFRACTION5E2 - 263
8X-RAY DIFFRACTION5E301
9X-RAY DIFFRACTION6F10 - 70
10X-RAY DIFFRACTION7G2 - 263
11X-RAY DIFFRACTION7G301
12X-RAY DIFFRACTION8H11 - 70

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