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

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Basic information

Entry
Database: PDB / ID: 9cgw
TitleStructure of the alpha-N-methyltransferase (SonM) and RiPP precursor (SonA-I65W) heteromeric complex (no cofactor)
Components
  • Extradiol ring-cleavage dioxygenase LigAB LigA subunit domain-containing protein
  • TP-methylase family protein
KeywordsTRANSFERASE / alpha-N-methyltransferase
Function / homologyDioxygenase LigAB, LigA subunit superfamily / Tetrapyrrole methylase / Tetrapyrrole (Corrin/Porphyrin) Methylases / Tetrapyrrole methylase, subdomain 1 / Tetrapyrrole methylase superfamily / methyltransferase activity / metal ion binding / Uncharacterized protein / TP-methylase family protein
Function and homology information
Biological speciesShewanella oneidensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 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)75,9145
Polymers75,8484
Non-polymers651
Water27015
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9350 Å2
ΔGint-100 kcal/mol
Surface area25040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.810, 91.810, 161.170
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein TP-methylase family protein


Mass: 29068.326 Da / Num. of mol.: 2
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
#2: Protein Extradiol ring-cleavage dioxygenase LigAB LigA subunit domain-containing protein


Mass: 8855.729 Da / Num. of mol.: 2 / Mutation: I65W
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
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 2.59 Å3/Da / Density % sol: 52.42 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 240 mM sodium malonate pH 5.5 with 10% 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: Mar 3, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.65→45.9 Å / Num. obs: 23018 / % possible obs: 99.7 % / Redundancy: 7.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.155 / Net I/σ(I): 13.39
Reflection shellResolution: 2.65→2.75 Å / Num. unique obs: 2397 / CC1/2: 0.504 / Rrim(I) all: 1.717

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→45.9 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.903 / SU B: 34.468 / SU ML: 0.312 / Cross valid method: THROUGHOUT / ESU R: 0.8 / ESU R Free: 0.356 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28019 1151 5 %RANDOM
Rwork0.2214 ---
obs0.22429 21865 98.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 67.617 Å2
Baniso -1Baniso -2Baniso -3
1--0.43 Å2-0.21 Å2-0 Å2
2---0.43 Å20 Å2
3---1.38 Å2
Refinement stepCycle: 1 / Resolution: 2.65→45.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4772 0 1 15 4788
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0010.0124883
X-RAY DIFFRACTIONr_bond_other_d00.0164647
X-RAY DIFFRACTIONr_angle_refined_deg0.5741.8136635
X-RAY DIFFRACTIONr_angle_other_deg0.191.74210702
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3535608
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.952520
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.71310816
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0260.2750
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.025715
X-RAY DIFFRACTIONr_gen_planes_other00.021085
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_it4.0675.4352444
X-RAY DIFFRACTIONr_mcbond_other4.0675.4362444
X-RAY DIFFRACTIONr_mcangle_it6.1749.7553045
X-RAY DIFFRACTIONr_mcangle_other6.1769.7573046
X-RAY DIFFRACTIONr_scbond_it5.3786.0382439
X-RAY DIFFRACTIONr_scbond_other5.3776.042440
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.45310.8273590
X-RAY DIFFRACTIONr_long_range_B_refined11.88753.265468
X-RAY DIFFRACTIONr_long_range_B_other11.89953.275469
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.65→2.719 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 83 -
Rwork0.326 1585 -
obs--99.58 %
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)
10.47350.02520.03050.29020.23910.8596-0.0556-0.00390.04140.01080.02470.069-0.0063-0.0290.03090.1163-0.0401-0.01650.05040.01190.022438.65-10.304-9.863
25.40330.13230.9012.9656-0.54142.61390.1020.13170.2280.0113-0.06240.2629-0.1205-0.0354-0.03960.1167-0.03860.00260.0607-0.00130.032929.686-21.87613.624
30.5937-0.1114-0.0880.6467-0.04430.38650.0154-0.0132-0.0183-0.03320.0064-0.17320.01310.0814-0.02180.0878-0.02230.00250.0535-0.01040.055455.045-20.338-11.733
46.5762-1.2574-0.29951.6816-0.07091.1681-0.0159-0.11840.8503-0.01290.2414-0.60930.09770.1402-0.22550.0749-0.0414-0.05060.0969-0.08660.311269.44-5.7027.243
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 262
2X-RAY DIFFRACTION2B10 - 54
3X-RAY DIFFRACTION3C2 - 260
4X-RAY DIFFRACTION4D11 - 54

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