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- PDB-7rc6: Aeronamide N-methyltransferase, AerE, bound to modified peptide s... -

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Basic information

Entry
Database: PDB / ID: 7rc6
TitleAeronamide N-methyltransferase, AerE, bound to modified peptide substrate, AerA-DL,34
Components
  • Aeronamide A peptide
  • Methyltransferase family protein
KeywordsTRANSFERASE/BIOSYNTHETIC PROTEIN / SAM-dependent / peptide cytotoxin / proteusin / BIOSYNTHETIC PROTEIN / TRANSFERASE-BIOSYNTHETIC PROTEIN complex
Function / homology
Function and homology information


eRF1 methyltransferase complex / protein methyltransferase activity / S-adenosylmethionine-dependent methyltransferase activity / methylation
Similarity search - Function
: / Methyltransferase small domain / Methyltransferase small domain / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / Methyltransferase family protein
Similarity search - Component
Biological speciesMicrovirgula aerodenitrificans DSM 15089 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 Å
AuthorsCogan, D.P. / Reyes, R. / Nair, S.K.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: Structure and mechanism for iterative amide N -methylation in the biosynthesis of channel-forming peptide cytotoxins.
Authors: Cogan, D.P. / Bhushan, A. / Reyes, R. / Zhu, L. / Piel, J. / Nair, S.K.
History
DepositionJul 7, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2022Provider: 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 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 2.0Dec 25, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_validate_close_contact / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _chem_comp.mon_nstd_flag / _chem_comp.type / _pdbx_entry_details.has_protein_modification / _pdbx_nonpoly_scheme.auth_seq_num

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Methyltransferase family protein
C: Aeronamide A peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4734
Polymers45,0662
Non-polymers4072
Water9,854547
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2190 Å2
ΔGint-21 kcal/mol
Surface area16060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.029, 78.029, 153.399
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-650-

HOH

21A-885-

HOH

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Components

#1: Protein Methyltransferase family protein


Mass: 42007.539 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Microvirgula aerodenitrificans DSM 15089 (bacteria)
Gene: aerE / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A329B7M1
#2: Protein/peptide Aeronamide A peptide / AerA-DL


Mass: 3058.358 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Microvirgula aerodenitrificans DSM 15089 (bacteria)
Gene: aerA / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 547 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.99 Å3/Da / Density % sol: 58.88 %
Crystal growTemperature: 282 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 18% PEG 3350, 0.1 M sodium citrate pH 4.0, 0.2 M sodium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97856 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Oct 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.71→67.575 Å / Num. obs: 58778 / % possible obs: 100 % / Redundancy: 14.8 % / CC1/2: 1 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.023 / Net I/σ(I): 20
Reflection shellResolution: 1.715→1.744 Å / Redundancy: 11.1 % / Rmerge(I) obs: 1.047 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2903 / CC1/2: 0.805 / Rpim(I) all: 0.327 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7RC2

7rc2


Resolution: 1.71→40.78 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1876 3006 5.12 %
Rwork0.165 55716 -
obs0.1662 58722 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 79.81 Å2 / Biso mean: 24.0548 Å2 / Biso min: 10.79 Å2
Refinement stepCycle: final / Resolution: 1.71→40.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2963 0 27 547 3537
Biso mean--16.21 37.77 -
Num. residues----386
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.71-1.740.28751300.268726172747100
1.74-1.770.29861330.240326602793100
1.77-1.810.2741420.210326202762100
1.81-1.840.20841440.205526102754100
1.84-1.880.20571390.1926142753100
1.88-1.920.22671450.176926162761100
1.92-1.960.21151410.168126282769100
1.96-2.010.19651540.168226012755100
2.01-2.070.21211280.175226682796100
2.07-2.130.17581290.171926372766100
2.13-2.20.19481700.172125782748100
2.2-2.270.17791520.165726502802100
2.27-2.370.16821620.159826382800100
2.37-2.470.18911290.158526332762100
2.47-2.60.19661400.167126932833100
2.6-2.770.1598990.168426832782100
2.77-2.980.1941450.162226542799100
2.98-3.280.19081410.168826942835100
3.28-3.750.16391270.147327282855100
3.75-4.730.16671950.13126662861100
4.73-40.780.18951610.17252828298999

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