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- PDB-7rc2: Aeronamide N-methyltransferase, AerE -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 7rc2
TitleAeronamide N-methyltransferase, AerE
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 / SAD / Resolution: 1.51 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 1.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)42,6495
Polymers42,0081
Non-polymers6424
Water9,998555
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)77.566, 77.566, 152.314
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-657-

HOH

21A-839-

HOH

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 559 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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 555 / 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: 3.15 Å3/Da / Density % sol: 60.94 %
Crystal growTemperature: 282 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 40% 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-D / Wavelength: 0.97851 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97851 Å / Relative weight: 1
ReflectionResolution: 1.508→67.174 Å / Num. obs: 84396 / % possible obs: 100 % / Redundancy: 20.2 % / CC1/2: 1 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.018 / Net I/σ(I): 23.2
Reflection shellResolution: 1.508→1.534 Å / Redundancy: 17.6 % / Rmerge(I) obs: 1.151 / Num. unique obs: 4170 / CC1/2: 0.854 / Rpim(I) all: 0.28 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.51→40.5 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 16.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1754 4259 5.05 %
Rwork0.1612 80122 -
obs0.162 84381 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 63.37 Å2 / Biso mean: 21.3822 Å2 / Biso min: 8.87 Å2
Refinement stepCycle: final / Resolution: 1.51→40.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2884 0 41 555 3480
Biso mean--19.38 34.95 -
Num. residues----373
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.51-1.520.2451090.227126732782
1.52-1.540.22731350.223526482783
1.54-1.560.22781530.210426232776
1.56-1.580.19221480.197326342782
1.58-1.60.20651450.194626122757
1.6-1.620.19131280.171326672795
1.62-1.650.20981380.171526772815
1.65-1.670.20331080.164326282736
1.67-1.70.19131580.16626222780
1.7-1.730.19491160.166627092825
1.73-1.760.1881370.168126082745
1.76-1.790.16991670.163326182785
1.79-1.820.19311630.169426312794
1.82-1.860.19141390.166326542793
1.86-1.90.16641560.161726522808
1.9-1.940.17761300.16426882818
1.94-1.990.17111420.156626342776
1.99-2.050.14731400.160126642804
2.05-2.110.1971400.156226462786
2.11-2.170.18831350.157426622797
2.17-2.250.16981140.152826922806
2.25-2.340.15741650.158526792844
2.34-2.450.17721420.151826682810
2.45-2.580.16191280.158727082836
2.58-2.740.15921630.163126612824
2.74-2.950.18591560.161826782834
2.95-3.250.18351750.16526852860
3.25-3.720.17851640.15227202884
3.72-4.680.12771220.133427682890
4.68-40.50.19311430.180329133056

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