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- PDB-7rc3: Aeronamide N-methyltransferase, AerE (Y137F) -

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Basic information

Entry
Database: PDB / ID: 7rc3
TitleAeronamide N-methyltransferase, AerE (Y137F)
ComponentsMethyltransferase family protein
KeywordsTRANSFERASE / SAM-dependent / peptide cytotoxin / proteusin
Function / homologyMethyltransferase small domain / Methyltransferase small domain / methyltransferase activity / methylation / S-adenosyl-L-methionine-dependent methyltransferase superfamily / ASPARTIC ACID / TRIETHYLENE GLYCOL / S-ADENOSYL-L-HOMOCYSTEINE / Methyltransferase family protein
Function and homology information
Biological speciesMicrovirgula aerodenitrificans DSM 15089 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsCogan, D.P. / Reyes, R. / Nair, S.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
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)43,2229
Polymers41,9921
Non-polymers1,2308
Water8,197455
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)77.697, 77.697, 152.239
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-677-

HOH

21A-818-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Methyltransferase family protein


Mass: 41991.539 Da / Num. of mol.: 1 / Mutation: Y137F
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 , 8 types, 463 molecules

#2: Chemical ChemComp-ASP / ASPARTIC ACID


Type: L-peptide linking / Mass: 133.103 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H7NO4
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: 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
#6: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C14H20N6O5S
#7: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 455 / 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: 3.16 Å3/Da / Density % sol: 61.06 %
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: Feb 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.526→67.287 Å / Num. obs: 81532 / % possible obs: 100 % / Redundancy: 17 % / CC1/2: 1 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.023 / Net I/σ(I): 17
Reflection shellResolution: 1.526→1.553 Å / Redundancy: 15.6 % / Rmerge(I) obs: 1.296 / Num. unique obs: 4014 / CC1/2: 0.776 / % 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: 1.53→19.52 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 16.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.184 4009 4.98 %
Rwork0.1642 76513 -
obs0.1651 80522 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 64.4 Å2 / Biso mean: 20.6858 Å2 / Biso min: 10.74 Å2
Refinement stepCycle: final / Resolution: 1.53→19.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2866 0 79 455 3400
Biso mean--26.88 33.55 -
Num. residues----373
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 29 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.53-1.550.23651520.220125902742
1.55-1.570.22371380.212826052743
1.57-1.590.23881580.198825532711
1.59-1.610.22221420.201326222764
1.61-1.630.21961430.191325842727
1.63-1.660.20291510.178226272778
1.66-1.680.20911500.182425762726
1.68-1.710.1881360.168926062742
1.71-1.730.22381050.178626242729
1.73-1.760.19281410.168926252766
1.76-1.80.19391390.167426122751
1.8-1.830.18571320.176726252757
1.83-1.870.17311490.168126002749
1.87-1.910.18061050.157126342739
1.91-1.950.19551230.157526642787
1.95-20.18251510.161325962747
2-2.060.16921540.1626232777
2.06-2.120.17461160.161526482764
2.12-2.180.17691310.159826462777
2.18-2.260.15231340.152126292763
2.26-2.350.19841380.156726482786
2.35-2.460.16791210.157526312752
2.46-2.590.17071300.16127032833
2.59-2.750.19581470.167326322779
2.75-2.960.18891550.168126312786
2.96-3.260.19591620.172626772839
3.26-3.730.17141510.155726782829
3.73-4.690.13241110.139427572868
4.69-19.520.21211440.178328673011

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