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- PDB-7ltr: Structure of the heteromeric complex between the alpha-N-methyltr... -

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Basic information

Entry
Database: PDB / ID: 7ltr
TitleStructure of the heteromeric complex between the alpha-N-methyltransferase (SonM) and a truncated construct of the RiPP precursor (SonA) (with SAM)
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
S-ADENOSYLMETHIONINE / Uncharacterized protein / TP-methylase family protein
Similarity search - Component
Biological speciesShewanella oneidensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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
H: TP-methylase family protein
I: LigA domain-containing protein
J: TP-methylase family protein
K: LigA domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,72914
Polymers147,5648
Non-polymers1,1656
Water17,871992
1
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)74,3647
Polymers73,7824
Non-polymers5833
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9870 Å2
ΔGint-60 kcal/mol
Surface area25100 Å2
MethodPISA
2
H: TP-methylase family protein
I: LigA domain-containing protein
J: TP-methylase family protein
K: LigA domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,3647
Polymers73,7824
Non-polymers5833
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9880 Å2
ΔGint-58 kcal/mol
Surface area24890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.240, 112.860, 85.870
Angle α, β, γ (deg.)90.000, 97.820, 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.: 4
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: 7822.600 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: truncated construct of the RiPP precursor (SonA) / Source: (gene. exp.) Shewanella oneidensis (bacteria) / Strain: MR-1 / Gene: SO_1479 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8EGW2
#3: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 992 / 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: 2.35 Å3/Da / Density % sol: 47.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: proteins at 20 mg/mL and crystallized in 100 mM Bis-Tris at pH 5.5 with 100 mM ammonium acetate and 4-7% PEG 10000

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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: 1.75→56.43 Å / Num. obs: 134823 / % possible obs: 98.3 % / Redundancy: 4.29 % / CC1/2: 0.983 / Net I/σ(I): 24.88
Reflection shellResolution: 1.75→1.85 Å / Num. unique obs: 20453 / CC1/2: 0.974

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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: 1.75→56.43 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.947 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.121 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.219 6742 5 %RANDOM
Rwork0.1873 ---
obs0.1889 128081 98.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 110.6 Å2 / Biso mean: 30.189 Å2 / Biso min: 8.91 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å20.01 Å2
2---0.01 Å2-0 Å2
3----0.06 Å2
Refinement stepCycle: final / Resolution: 1.75→56.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9753 0 78 993 10824
Biso mean--33.76 44.75 -
Num. residues----1252
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.01310166
X-RAY DIFFRACTIONr_bond_other_d0.0350.0179638
X-RAY DIFFRACTIONr_angle_refined_deg1.1231.63513841
X-RAY DIFFRACTIONr_angle_other_deg2.2591.57422211
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.05251282
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.56123.594512
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.876151691
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7661546
X-RAY DIFFRACTIONr_chiral_restr0.0450.21334
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0211703
X-RAY DIFFRACTIONr_gen_planes_other0.0040.022289
LS refinement shellResolution: 1.75→1.795 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.396 493 -
Rwork0.389 9354 -
all-9847 -
obs--97.31 %

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