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- PDB-7lth: Structure of the alpha-N-methyltransferase (SonM mutant Y93F) and... -

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Basic information

Entry
Database: PDB / ID: 7lth
TitleStructure of the alpha-N-methyltransferase (SonM mutant Y93F) 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 / metal ion binding
Similarity search - Function
Dioxygenase LigAB, LigA subunit superfamily / Tetrapyrrole methylase, N-terminal domain / Cobalt-precorrin-4 Transmethylase; domain 1 / Tetrapyrrole methylase / Tetrapyrrole (Corrin/Porphyrin) Methylases / Tetrapyrrole methylase, subdomain 1 / Tetrapyrrole methylase superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Uncharacterized protein / TP-methylase family protein
Similarity search - Component
Biological speciesShewanella oneidensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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
Revision 1.2Oct 9, 2024Group: Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag

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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: 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
Water18,1411007
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13780 Å2
ΔGint-79 kcal/mol
Surface area24280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.340, 108.710, 58.960
Angle α, β, γ (deg.)90.000, 93.920, 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: Y93F
Source method: isolated from a genetically manipulated source
Details: SonM mutant Y93F / 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


Mass: 18.015 Da / Num. of mol.: 1007 / 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: 2.27 Å3/Da / Density % sol: 45.75 %
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: 2.1→58.82 Å / Num. obs: 38054 / % possible obs: 99.2 % / Redundancy: 5.41 % / CC1/2: 0.998 / Net I/σ(I): 17.5
Reflection shellResolution: 2.1→2.2 Å / Num. unique obs: 4943 / CC1/2: 0.997

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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: 2.1→58.82 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.944 / SU B: 4.3 / SU ML: 0.115 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.289 / ESU R Free: 0.203 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2292 1903 5 %RANDOM
Rwork0.1832 ---
obs0.1855 36150 99.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 117.74 Å2 / Biso mean: 20.587 Å2 / Biso min: 7.37 Å2
Baniso -1Baniso -2Baniso -3
1--1.14 Å2-0 Å20.19 Å2
2--2.43 Å20 Å2
3----1.3 Å2
Refinement stepCycle: final / Resolution: 2.1→58.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5138 0 0 1007 6145
Biso mean---39.1 -
Num. residues----661
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0135296
X-RAY DIFFRACTIONr_bond_other_d0.0020.0174980
X-RAY DIFFRACTIONr_angle_refined_deg1.6461.6357207
X-RAY DIFFRACTIONr_angle_other_deg1.4461.57311471
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7245667
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.82723.745267
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.92115866
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.8421522
X-RAY DIFFRACTIONr_chiral_restr0.0750.2687
X-RAY DIFFRACTIONr_gen_planes_refined0.010.026161
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021189
LS refinement shellResolution: 2.1→2.155 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 139 -
Rwork0.21 2647 -
all-2786 -
obs--99.36 %

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