[English] 日本語
Yorodumi
- PDB-7rc3: Aeronamide N-methyltransferase, AerE (Y137F) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7rc3
TitleAeronamide N-methyltransferase, AerE (Y137F)
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
ASPARTIC ACID / TRIETHYLENE GLYCOL / S-ADENOSYL-L-HOMOCYSTEINE / Methyltransferase family protein
Similarity search - Component
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
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

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more