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- PDB-7lte: Structure of the alpha-N-methyltransferase (SonM) and RiPP precur... -

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Basic information

Entry
Database: PDB / ID: 7lte
TitleStructure of the alpha-N-methyltransferase (SonM) 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
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
S-ADENOSYL-L-HOMOCYSTEINE / 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 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,6076
Polymers73,8384
Non-polymers7692
Water18,8081044
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13740 Å2
ΔGint-79 kcal/mol
Surface area23970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.460, 108.660, 59.090
Angle α, β, γ (deg.)90.000, 94.100, 90.000
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) / 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: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / 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 / Water


Mass: 18.015 Da / Num. of mol.: 1044 / 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: 2.28 Å3/Da / Density % sol: 45.94 %
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→58.94 Å / Num. obs: 42332 / % possible obs: 94.6 % / Redundancy: 3.18 % / CC1/2: 0.997 / Net I/σ(I): 14.49
Reflection shellResolution: 2→2.1 Å / Num. unique obs: 6106 / CC1/2: 0.991

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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→58.94 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.937 / SU B: 4.266 / SU ML: 0.119 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.287 / ESU R Free: 0.201 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2444 2095 5 %RANDOM
Rwork0.2121 ---
obs0.2137 39805 93.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 129.98 Å2 / Biso mean: 19.844 Å2 / Biso min: 4.51 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20 Å2-0.65 Å2
2--1.15 Å20 Å2
3----1.19 Å2
Refinement stepCycle: final / Resolution: 2→58.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5140 0 52 1044 6236
Biso mean--15.63 39.23 -
Num. residues----661
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0135346
X-RAY DIFFRACTIONr_bond_other_d0.0030.0175008
X-RAY DIFFRACTIONr_angle_refined_deg1.4081.6377278
X-RAY DIFFRACTIONr_angle_other_deg1.3221.57511538
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6035665
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.61623.759266
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.38215865
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.1751522
X-RAY DIFFRACTIONr_chiral_restr0.0690.2696
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.026209
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021191
LS refinement shellResolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 159 -
Rwork0.227 3008 -
all-3167 -
obs--96.44 %

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