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- PDB-8t1s: Structure of the alpha-N-methyltransferase (SonM) and RiPP precur... -

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Basic information

Entry
Database: PDB / ID: 8t1s
TitleStructure of the alpha-N-methyltransferase (SonM) and RiPP precursor (SonA with QSY deletion) heteromeric complex (bound to SAH)
Components
  • Alpha-N-methyltransferase
  • Extradiol ring-cleavage dioxygenase LigAB LigA subunit domain-containing protein
KeywordsTRANSFERASE / alpha-N-methyltransferase / borosin / natural products.
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. / Jomori, T. / Miller, F.S. / Gralnick, J. / Elias, M. / Freeman, M.F.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM133475 United States
CitationJournal: Rsc Chem Biol / Year: 2023
Title: RiPP enzyme heterocomplex structure-guided discovery of a bacterial borosin alpha- N -methylated peptide natural product.
Authors: Crone, K.K. / Jomori, T. / Miller, F.S. / Gralnick, J.A. / Elias, M.H. / Freeman, M.F.
History
DepositionJun 3, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.mon_nstd_flag / _chem_comp.type / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha-N-methyltransferase
B: Extradiol ring-cleavage dioxygenase LigAB LigA subunit domain-containing protein
C: Alpha-N-methyltransferase
D: Extradiol ring-cleavage dioxygenase LigAB LigA subunit domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,5457
Polymers74,7114
Non-polymers8343
Water9,800544
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12440 Å2
ΔGint-120 kcal/mol
Surface area23870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.390, 108.730, 59.140
Angle α, β, γ (deg.)90.00, 93.66, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Alpha-N-methyltransferase / SonM


Mass: 28937.131 Da / Num. of mol.: 2
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 Extradiol ring-cleavage dioxygenase LigAB LigA subunit domain-containing protein / RiPP precursor / SonA


Mass: 8418.323 Da / Num. of mol.: 2 / Mutation: Deletion of QSY residues.
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: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 544 / 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: 2.22 Å3/Da / Density % sol: 44.6 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop
Details: 240 mM sodium malonate pH 5-5.5, 8-12% PEG 3350 at a 1-1 or 2-1 ratio of protein to mother liquor. Protein concentration is 20mg/mL.

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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 X 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→52.28 Å / Num. obs: 44465 / % possible obs: 99.7 % / Redundancy: 5.41 % / CC1/2: 0.997 / Rrim(I) all: 0.111 / Net I/σ(I): 10.89
Reflection shellResolution: 2→2.1 Å / Num. unique obs: 6044 / CC1/2: 1 / Rrim(I) all: 0.582

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→52.28 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.941 / SU B: 4.651 / SU ML: 0.13 / Cross valid method: THROUGHOUT / ESU R: 0.221 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23814 2224 5 %RANDOM
Rwork0.20273 ---
obs0.2045 42244 99.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.852 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å2-0 Å2-0.08 Å2
2---0.28 Å2-0 Å2
3---0.23 Å2
Refinement stepCycle: 1 / Resolution: 2→52.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5032 0 1 544 5577
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0125208
X-RAY DIFFRACTIONr_bond_other_d0.0110.0164734
X-RAY DIFFRACTIONr_angle_refined_deg0.5531.6437090
X-RAY DIFFRACTIONr_angle_other_deg0.2921.56111056
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2145648
X-RAY DIFFRACTIONr_dihedral_angle_2_deg1.641522
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.74610852
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0280.2796
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.025889
X-RAY DIFFRACTIONr_gen_planes_other00.02977
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_it1.8572.492588
X-RAY DIFFRACTIONr_mcbond_other1.8552.492587
X-RAY DIFFRACTIONr_mcangle_it2.6863.7163227
X-RAY DIFFRACTIONr_mcangle_other2.6863.7173228
X-RAY DIFFRACTIONr_scbond_it3.0242.8922620
X-RAY DIFFRACTIONr_scbond_other3.0242.8922621
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.6564.1843859
X-RAY DIFFRACTIONr_long_range_B_refined7.40741.1286123
X-RAY DIFFRACTIONr_long_range_B_other7.21339.0316016
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 165 -
Rwork0.255 3123 -
obs--100 %

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