[English] 日本語
Yorodumi
- PDB-6nvm: Crystal structure of 23S rRNA methyltransferase ErmE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6nvm
TitleCrystal structure of 23S rRNA methyltransferase ErmE
ComponentsrRNA adenine N-6-methyltransferase
KeywordsTRANSFERASE / ErmE / rRNA methyltransferase
Function / homology
Function and homology information


23S rRNA (adenine2085-N6)-dimethyltransferase / 23S rRNA (adenine(2085)-N(6))-dimethyltransferase activity / rRNA (adenine-N6,N6-)-dimethyltransferase activity / response to antibiotic / RNA binding
Similarity search - Function
Ribosomal RNA adenine methylase transferase, conserved site / Ribosomal RNA adenine methylase transferase, N-terminal / Ribosomal RNA adenine dimethylases signature. / Ribosomal RNA adenine dimethylases / Ribosomal RNA adenine methyltransferase KsgA/Erm / Ribosomal RNA adenine dimethylase / rRNA adenine N(6)-methyltransferase family profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
rRNA adenine N-6-methyltransferase
Similarity search - Component
Biological speciesSaccharopolyspora erythraea (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å
AuthorsStsiapanava, A. / Selmer, M.
Funding support Sweden, 2items
OrganizationGrant numberCountry
Swedish Research Council2017-03827 Sweden
Swedish Research Council2016-06264 Sweden
CitationJournal: Sci Rep / Year: 2019
Title: Crystal structure of ErmE - 23S rRNA methyltransferase in macrolide resistance.
Authors: Stsiapanava, A. / Selmer, M.
History
DepositionFeb 5, 2019Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 9, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2019Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.year
Revision 1.2Nov 20, 2019Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.process_site

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: rRNA adenine N-6-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9232
Polymers34,8271
Non-polymers961
Water3,729207
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area180 Å2
ΔGint-13 kcal/mol
Surface area12160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.040, 76.040, 104.920
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-437-

HOH

-
Components

#1: Protein rRNA adenine N-6-methyltransferase / NMT / Erythromycin resistance protein / Macrolide-lincosamide-streptogramin B resistance protein


Mass: 34826.645 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The first residue in the coordinate sequence is Asn42. Thus, the numbering of residues in the sample sequence begins with Met, which follows the His-tag
Source: (gene. exp.) Saccharopolyspora erythraea (bacteria) / Gene: ermE, SACE_0733 / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): AI
References: UniProt: P07287, 23S rRNA (adenine2085-N6)-dimethyltransferase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 207 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.74 Å3/Da / Density % sol: 55.12 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 2% (v/v) Tacsimate pH 5.0, 0.1 M Sodium citrate tribasic dihydrate pH 5.6 and 16% (w/v) PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Nov 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.75→37.549 Å / Num. obs: 31708 / % possible obs: 99.91 % / Redundancy: 15 % / Biso Wilson estimate: 34.07 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.025 / Rrim(I) all: 0.096 / Net I/σ(I): 19.04
Reflection shellResolution: 1.75→1.81 Å / Mean I/σ(I) obs: 0.77 / Num. unique obs: 3116 / CC1/2: 0.324 / % possible all: 99.84

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→37.549 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.98
RfactorNum. reflection% reflection
Rfree0.2185 1829 5.77 %
Rwork0.192 --
obs0.1935 31695 99.92 %
Solvent computationShrinkage radii: 0.7 Å / VDW probe radii: 1 Å
Refinement stepCycle: LAST / Resolution: 1.75→37.549 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1949 0 5 207 2161
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042096
X-RAY DIFFRACTIONf_angle_d0.5862855
X-RAY DIFFRACTIONf_dihedral_angle_d8.5261287
X-RAY DIFFRACTIONf_chiral_restr0.045309
X-RAY DIFFRACTIONf_plane_restr0.004379
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.79740.38711380.37452244X-RAY DIFFRACTION100
1.7974-1.85020.34651390.34082270X-RAY DIFFRACTION100
1.8502-1.910.32691370.30352234X-RAY DIFFRACTION100
1.91-1.97820.3791390.29542263X-RAY DIFFRACTION100
1.9782-2.05740.25661400.2362275X-RAY DIFFRACTION100
2.0574-2.1510.23871380.21892261X-RAY DIFFRACTION100
2.151-2.26440.2381410.2082275X-RAY DIFFRACTION100
2.2644-2.40630.21111390.18332285X-RAY DIFFRACTION100
2.4063-2.5920.22681410.18082289X-RAY DIFFRACTION100
2.592-2.85280.21191400.18062297X-RAY DIFFRACTION100
2.8528-3.26540.20381420.18292328X-RAY DIFFRACTION100
3.2654-4.11330.18521440.15942346X-RAY DIFFRACTION100
4.1133-37.55750.20031510.18252499X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.64760.4421-0.11371.0575-0.73261.61340.0119-0.0023-0.0321-0.0018-0.0373-0.08920.13620.120500.2630.0128-0.0060.29170.00440.30016.759149.994223.3341
21.31220.4925-0.54670.5259-0.48030.4499-0.070.4105-0.0174-0.19910.11970.05220.0102-0.1168-00.3453-0.0102-0.02480.44840.02720.340415.231869.6875-0.502
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and resi 42-216A42 - 216
2X-RAY DIFFRACTION2chain A and resi 217-285A217 - 285

+
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