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- PDB-7ltf: Structure of the alpha-N-methyltransferase (SonM mutant Y58F) and... -

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Basic information

Entry
Database: PDB / ID: 7ltf
TitleStructure of the alpha-N-methyltransferase (SonM mutant Y58F) and RiPP precursor (SonA) heteromeric complex (no cofactor)
Components
  • LigA domain-containing protein
  • TP-methylase family protein
KeywordsTRANSFERASE / posttranslational modifications / ribosomally synthesized and posttranslationally modified peptides / alpha-N-methyltransferase / borosin / SAM
Function / homology
Function and homology information


methyltransferase activity
Similarity search - Function
Extradiol ring-cleavage dioxygenase LigAB, LigA subunit / Dioxygenase LigAB, LigA subunit superfamily / Aromatic-ring-opening dioxygenase LigAB, LigA subunit / Tetrapyrrole methylase / Tetrapyrrole (Corrin/Porphyrin) Methylases / Tetrapyrrole methylase, subdomain 1 / Tetrapyrrole methylase superfamily
Similarity search - Domain/homology
Extradiol ring-cleavage dioxygenase LigAB LigA subunit domain-containing protein / TP-methylase family protein
Similarity search - Component
Biological speciesShewanella oneidensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsMiller, F.S. / Crone, K.K. / Jensen, M.R. / Shaw, S. / Harcombe, W.R. / 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: Nat Commun / Year: 2021
Title: Conformational rearrangements enable iterative backbone N-methylation in RiPP biosynthesis.
Authors: Miller, F.S. / Crone, K.K. / Jensen, M.R. / Shaw, S. / Harcombe, W.R. / Elias, M.H. / Freeman, M.F.
History
DepositionFeb 19, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 29, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TP-methylase family protein
B: LigA domain-containing protein
C: TP-methylase family protein
D: LigA domain-containing protein


Theoretical massNumber of molelcules
Total (without water)73,8064
Polymers73,8064
Non-polymers00
Water9,332518
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13820 Å2
ΔGint-78 kcal/mol
Surface area24100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.370, 108.500, 58.950
Angle α, β, γ (deg.)90.000, 94.130, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein TP-methylase family protein


Mass: 29052.326 Da / Num. of mol.: 2 / Mutation: Y58F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella oneidensis (bacteria) / Strain: MR-1 / Gene: SO_1478 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8EGW3
#2: Protein LigA domain-containing protein


Mass: 7850.653 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella oneidensis (bacteria) / Strain: MR-1 / Gene: SO_1479 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8EGW2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 518 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.26 Å3/Da / Density % sol: 45.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Proteins were concentrated at 20 mg/mL and crystallized at pH ranging between 5.5-7 and using PEG 3,350 (0-20%) as precipitant

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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: Mar 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033167 Å / Relative weight: 1
ReflectionResolution: 2.2→58.8 Å / Num. obs: 33041 / % possible obs: 99.1 % / Redundancy: 4.61 % / CC1/2: 0.991 / Net I/σ(I): 15.48
Reflection shellResolution: 2.2→2.3 Å / Num. unique obs: 4031 / CC1/2: 0.978

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Processing

Software
NameVersionClassification
REFMACv5refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5N0P
Resolution: 2.2→58.8 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2376 --RANDOM
Rwork0.2255 ---
obs-31389 99.07 %-
Displacement parametersBiso max: 125.31 Å2 / Biso mean: 26.4867 Å2 / Biso min: 8.88 Å2
Refinement stepCycle: LAST / Resolution: 2.2→58.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5134 0 0 518 5652

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