[English] 日本語
Yorodumi
- PDB-9ch3: Structure of the alpha-N-methyltransferase (SonM) and RiPP precur... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9ch3
TitleStructure of the alpha-N-methyltransferase (SonM) and RiPP precursor (SonA-L63D) heteromeric complex (bound to SAH)
Components
  • (Extradiol ring-cleavage dioxygenase LigAB LigA subunit domain-containing ...) x 2
  • TP-methylase family protein
KeywordsTRANSFERASE / Alpha-N-methyltransferase
Function / homology
Function and homology information


methyltransferase activity / metal ion binding
Similarity search - Function
Dioxygenase LigAB, LigA subunit superfamily / Tetrapyrrole methylase / Tetrapyrrole (Corrin/Porphyrin) Methylases / Tetrapyrrole methylase, subdomain 1 / Tetrapyrrole methylase superfamily
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / Uncharacterized protein / TP-methylase family protein
Similarity search - Component
Biological speciesShewanella oneidensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsCrone, K.K. / Labonte, J.W. / Elias, M. / Freeman, M.F.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM133475 United States
CitationJournal: Protein Sci. / Year: 2025
Title: alpha-N-Methyltransferase regiospecificity is mediated by proximal, redundant enzyme-substrate interactions.
Authors: Crone, K.K. / Labonte, J.W. / Elias, M.H. / Freeman, M.F.
History
DepositionJul 1, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TP-methylase family protein
B: Extradiol ring-cleavage dioxygenase LigAB LigA subunit domain-containing protein
C: TP-methylase family protein
D: Extradiol ring-cleavage dioxygenase LigAB LigA subunit domain-containing protein
H: TP-methylase family protein
I: Extradiol ring-cleavage dioxygenase LigAB LigA subunit domain-containing protein
J: TP-methylase family protein
K: Extradiol ring-cleavage dioxygenase LigAB LigA subunit domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,09414
Polymers151,4268
Non-polymers1,6686
Water3,297183
1
A: TP-methylase family protein
B: Extradiol ring-cleavage dioxygenase LigAB LigA subunit domain-containing protein
C: TP-methylase family protein
D: Extradiol ring-cleavage dioxygenase LigAB LigA subunit domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,5547
Polymers75,7204
Non-polymers8343
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12260 Å2
ΔGint-112 kcal/mol
Surface area23570 Å2
MethodPISA
2
H: TP-methylase family protein
I: Extradiol ring-cleavage dioxygenase LigAB LigA subunit domain-containing protein
J: TP-methylase family protein
K: Extradiol ring-cleavage dioxygenase LigAB LigA subunit domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,5407
Polymers75,7064
Non-polymers8343
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11770 Å2
ΔGint-112 kcal/mol
Surface area23870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.000, 108.400, 59.000
Angle α, β, γ (deg.)90.00, 93.70, 90.20
Int Tables number1
Space group name H-MP1

-
Components

-
Protein , 1 types, 4 molecules ACHJ

#1: Protein
TP-methylase family protein


Mass: 29068.326 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella oneidensis (bacteria) / Gene: SO_1478 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8EGW3

-
Extradiol ring-cleavage dioxygenase LigAB LigA subunit domain-containing ... , 2 types, 4 molecules BDIK

#2: Protein Extradiol ring-cleavage dioxygenase LigAB LigA subunit domain-containing protein


Mass: 8798.634 Da / Num. of mol.: 1 / Mutation: L63D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella oneidensis (bacteria) / Gene: SO_1479 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8EGW2
#3: Protein Extradiol ring-cleavage dioxygenase LigAB LigA subunit domain-containing protein


Mass: 8784.607 Da / Num. of mol.: 3 / Mutation: L63D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella oneidensis (bacteria) / Gene: SO_1479 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8EGW2

-
Non-polymers , 3 types, 189 molecules

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


Mass: 384.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.34 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 240 mM sodium malonate pH 5.5 with 12% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033167 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 14, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033167 Å / Relative weight: 1
ReflectionResolution: 2.3→19.94 Å / Num. obs: 48659 / % possible obs: 85.1 % / Redundancy: 2.27 % / CC1/2: 0.995 / Rrim(I) all: 0.138 / Net I/σ(I): 7.38
Reflection shellResolution: 2.3→2.4 Å / Num. unique obs: 6165 / CC1/2: 0.863 / Rrim(I) all: 0.605

-
Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→19.94 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.9 / SU B: 7.519 / SU ML: 0.193 / Cross valid method: THROUGHOUT / ESU R: 0.197 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Twinning operator(s) (twinning fraction(s)) used in refinement: -H,K,-L (0.595)
RfactorNum. reflection% reflectionSelection details
Rfree0.2989 2419 5 %RANDOM
Rwork0.27606 ---
obs0.27716 46239 84.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 31.831 Å2
Baniso -1Baniso -2Baniso -3
1--7.96 Å25.76 Å2-5.23 Å2
2--5.75 Å2-7.5 Å2
3---2.21 Å2
Refinement stepCycle: 1 / Resolution: 2.3→19.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10009 0 2 183 10194
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0010.01210237
X-RAY DIFFRACTIONr_bond_other_d00.0169656
X-RAY DIFFRACTIONr_angle_refined_deg0.6671.80913917
X-RAY DIFFRACTIONr_angle_other_deg0.2121.74222237
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.27551260
X-RAY DIFFRACTIONr_dihedral_angle_2_deg2.387540
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.547101675
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0290.21565
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0211978
X-RAY DIFFRACTIONr_gen_planes_other00.022266
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.0193.1155092
X-RAY DIFFRACTIONr_mcbond_other3.0193.1155092
X-RAY DIFFRACTIONr_mcangle_it4.4585.5836337
X-RAY DIFFRACTIONr_mcangle_other4.4585.5846338
X-RAY DIFFRACTIONr_scbond_it3.2473.4175145
X-RAY DIFFRACTIONr_scbond_other3.2463.4195146
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.9386.1577581
X-RAY DIFFRACTIONr_long_range_B_refined7.27932.0211604
X-RAY DIFFRACTIONr_long_range_B_other7.27632.0411595
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.351 Å
RfactorNum. reflection% reflection
Rfree0.289 155 -
Rwork0.264 3145 -
obs--78.25 %

+
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