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- PDB-7lts: Structure of the alpha-N-methyltransferase (SonM mutant R67A) and... -

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Basic information

Entry
Database: PDB / ID: 7lts
TitleStructure of the alpha-N-methyltransferase (SonM mutant R67A) and RiPP precursor (SonA) heteromeric complex (with SAH)
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 / 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: 2.32 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 20, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,9316
Polymers74,1624
Non-polymers7692
Water1,24369
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14230 Å2
ΔGint-87 kcal/mol
Surface area24970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.950, 80.950, 236.470
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein TP-methylase family protein


Mass: 28982.209 Da / Num. of mol.: 2 / Mutation: R67A
Source method: isolated from a genetically manipulated source
Details: SonM mutant R67A / 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: 8098.894 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: cloning artifact (Nter His tag) / Source: (gene. exp.) Shewanella oneidensis (bacteria) / Strain: MR-1 / Gene: SO_1479 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8EGW2
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 2.61 Å3/Da / Density % sol: 52.88 %
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: 0.99184 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: 0.99184 Å / Relative weight: 1
ReflectionResolution: 2.32→76.59 Å / Num. obs: 35110 / % possible obs: 99.9 % / Redundancy: 19.16 % / CC1/2: 0.999 / Net I/σ(I): 19.16
Reflection shellResolution: 2.32→2.45 Å / Num. unique obs: 5161 / CC1/2: 0.846

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Processing

Software
NameVersionClassification
REFMAC5.8.0266refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5N0P

5n0p


Resolution: 2.32→76.59 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.945 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.309 / ESU R Free: 0.233 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2478 1752 5 %RANDOM
Rwork0.1975 ---
obs0.2001 33274 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 143.27 Å2 / Biso mean: 53.526 Å2 / Biso min: 34.76 Å2
Baniso -1Baniso -2Baniso -3
1-0.32 Å2-0 Å2-0 Å2
2--0.32 Å2-0 Å2
3----0.65 Å2
Refinement stepCycle: final / Resolution: 2.32→76.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5168 0 52 69 5289
Biso mean--45.62 59.72 -
Num. residues----667
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0135350
X-RAY DIFFRACTIONr_bond_other_d0.0350.0174993
X-RAY DIFFRACTIONr_angle_refined_deg1.161.6327276
X-RAY DIFFRACTIONr_angle_other_deg2.2761.57311510
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2985665
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.72524.115260
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.86515869
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0231518
X-RAY DIFFRACTIONr_chiral_restr0.0470.2698
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.026166
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021186
LS refinement shellResolution: 2.32→2.38 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 127 -
Rwork0.336 2410 -
all-2537 -
obs--100 %

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