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- PDB-9ch5: Structure of the alpha-N-methyltransferase (SonM) and RiPP precur... -

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Basic information

Entry
Database: PDB / ID: 9ch5
TitleStructure of the alpha-N-methyltransferase (SonM) and RiPP precursor (SonA-L63D) heteromeric complex (bound to SAM)
Components
  • Extradiol ring-cleavage dioxygenase LigAB LigA subunit domain-containing protein
  • TP-methylase family 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 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)76,4756
Polymers75,7064
Non-polymers7692
Water8,773487
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10290 Å2
ΔGint-65 kcal/mol
Surface area24360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.480, 108.380, 59.150
Angle α, β, γ (deg.)90.00, 93.67, 90.00
Int Tables number4
Space group name H-MP1211

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


Mass: 384.411 Da / Num. of mol.: 2
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)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 487 / 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: 2.22 Å3/Da / Density % sol: 44.53 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 240 mM sodium malonate pH 5.5 with 2% 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 14, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033167 Å / Relative weight: 1
ReflectionResolution: 2→19.9 Å / Num. obs: 75115 / % possible obs: 85.6 % / Redundancy: 2.29 % / CC1/2: 0.998 / Rrim(I) all: 0.077 / Net I/σ(I): 9.19
Reflection shellResolution: 2→2.1 Å / Num. unique obs: 10193 / CC1/2: 0.907 / Rrim(I) all: 0.473

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→19.9 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 31.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2794 1987 4.94 %
Rwork0.2398 --
obs0.2418 40198 90.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4965 0 0 487 5452
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007
X-RAY DIFFRACTIONf_angle_d1.041
X-RAY DIFFRACTIONf_dihedral_angle_d11.424702
X-RAY DIFFRACTIONf_chiral_restr0.058782
X-RAY DIFFRACTIONf_plane_restr0.007902
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.25061510.19832989X-RAY DIFFRACTION99
2.05-2.110.2186600.21511272X-RAY DIFFRACTION42
2.11-2.170.24751310.19682968X-RAY DIFFRACTION98
2.17-2.240.22431460.17622881X-RAY DIFFRACTION97
2.24-2.320.21811060.17372096X-RAY DIFFRACTION69
2.32-2.410.22751660.17972967X-RAY DIFFRACTION98
2.41-2.520.23081350.2082952X-RAY DIFFRACTION98
2.52-2.650.25851520.23282890X-RAY DIFFRACTION96
2.65-2.820.28341830.23662900X-RAY DIFFRACTION96
2.82-3.030.26241450.25782954X-RAY DIFFRACTION98
3.03-3.340.30471560.27092991X-RAY DIFFRACTION99
3.34-3.820.32641290.27042581X-RAY DIFFRACTION86
3.82-4.80.33021610.24882812X-RAY DIFFRACTION93
4.8-19.90.27591660.27212958X-RAY DIFFRACTION97

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