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- PDB-7rc4: Aeronamide N-methyltransferase, AerE (D141A) -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 7rc4
TitleAeronamide N-methyltransferase, AerE (D141A)
ComponentsMethyltransferase family protein
KeywordsTRANSFERASE / SAM-dependent / peptide cytotoxin / proteusin
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: 1.66 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Methyltransferase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9117
Polymers41,9641
Non-polymers9476
Water6,864381
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.595, 77.595, 151.734
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-671-

HOH

21A-768-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Methyltransferase family protein


Mass: 41963.527 Da / Num. of mol.: 1 / Mutation: D141A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Microvirgula aerodenitrificans DSM 15089 (bacteria)
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A329B7M1

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Non-polymers , 6 types, 387 molecules

#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 381 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.14 Å3/Da / Density % sol: 60.86 %
Crystal growTemperature: 282 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 37.5% PEG 300, 0.1 M sodium cacodylate pH 6.5, 0.2 M calcium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Nov 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.659→67.199 Å / Num. obs: 61591 / % possible obs: 97.2 % / Redundancy: 17.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.025 / Net I/σ(I): 15.5
Reflection shellResolution: 1.659→1.688 Å / Redundancy: 13.6 % / Rmerge(I) obs: 1.186 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 3133 / CC1/2: 0.876 / Rpim(I) all: 0.331 / % 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: 1.66→40.41 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1884 2991 4.86 %
Rwork0.1704 58568 -
obs0.1713 61559 97.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 72 Å2 / Biso mean: 23.9829 Å2 / Biso min: 13.42 Å2
Refinement stepCycle: final / Resolution: 1.66→40.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2885 0 61 381 3327
Biso mean--24.73 36.16 -
Num. residues----374
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 (%)
1.66-1.690.27661230.24328422965100
1.69-1.720.28961210.216828202941100
1.72-1.750.2251330.202928622995100
1.75-1.780.19711410.182328292970100
1.78-1.820.21181760.183928152991100
1.82-1.860.19151440.183428212965100
1.86-1.90.18621490.169328372986100
1.9-1.950.19781310.162328622993100
1.95-20.18741590.160528252984100
2-2.060.18141300.157228652995100
2.06-2.120.19091180.16661866198466
2.12-2.20.18891390.15828773016100
2.2-2.290.19311500.159128482998100
2.29-2.390.19251560.160228603016100
2.39-2.520.17631630.164528302993100
2.52-2.660.19291680.169426492817100
2.7-2.880.18411370.170825722709100
2.88-3.170.19291390.177128983037100
3.17-3.630.16961340.16622729286393
3.63-4.570.1631450.153629613106100
4.58-40.410.20551350.187531003235100

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