[English] 日本語
Yorodumi
- PDB-6ifx: Crystal structure of chimeric KsgA with loop 12 from Erm -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ifx
TitleCrystal structure of chimeric KsgA with loop 12 from Erm
ComponentsRibosomal RNA small subunit methyltransferase A
KeywordsTRANSFERASE / Chimera / resistance / KsgA
Function / homology
Function and homology information


16S rRNA (adenine1518-N6/adenine1519-N6)-dimethyltransferase / 16S rRNA (adenine(1518)-N(6)/adenine(1519)-N(6))-dimethyltransferase activity / rRNA (adenine-N6,N6-)-dimethyltransferase activity / rRNA methylation / RNA binding / cytosol
Similarity search - Function
rRNA adenine dimethylase, C-terminal domain / rRNA adenine dimethylase-like, C-terminal / Ribosomal RNA adenine dimethylase / 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. ...rRNA adenine dimethylase, C-terminal domain / rRNA adenine dimethylase-like, C-terminal / Ribosomal RNA adenine dimethylase / 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. / Helicase, Ruva Protein; domain 3 / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Ribosomal RNA small subunit methyltransferase A
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.8 Å
AuthorsBhujbalrao, R. / Anand, R.
Funding support India, 2items
OrganizationGrant numberCountry
Department of Science & Technology (India)SERB/F/4395/2016-17 India
Other government20150237B02RP00614-BRNS India
CitationJournal: J. Am. Chem. Soc. / Year: 2019
Title: Deciphering Determinants in Ribosomal Methyltransferases That Confer Antimicrobial Resistance.
Authors: Bhujbalrao, R. / Anand, R.
History
DepositionSep 21, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 13, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ribosomal RNA small subunit methyltransferase A
B: Ribosomal RNA small subunit methyltransferase A


Theoretical massNumber of molelcules
Total (without water)64,6512
Polymers64,6512
Non-polymers00
Water362
1
A: Ribosomal RNA small subunit methyltransferase A


Theoretical massNumber of molelcules
Total (without water)32,3261
Polymers32,3261
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ribosomal RNA small subunit methyltransferase A


Theoretical massNumber of molelcules
Total (without water)32,3261
Polymers32,3261
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.693, 79.499, 130.115
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ILE / Beg label comp-ID: ILE / End auth comp-ID: TYR / End label comp-ID: TYR / Refine code: _ / Auth seq-ID: 9 - 283 / Label seq-ID: 9 - 283

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

-
Components

#1: Protein Ribosomal RNA small subunit methyltransferase A / 16S rRNA (adenine(1518)-N(6)/adenine(1519)-N(6))-dimethyltransferase / 16S rRNA dimethyladenosine ...16S rRNA (adenine(1518)-N(6)/adenine(1519)-N(6))-dimethyltransferase / 16S rRNA dimethyladenosine transferase / 16S rRNA dimethylase / S-adenosylmethionine-6-N' / N'-adenosyl(rRNA) dimethyltransferase


Mass: 32325.559 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Chimeric construct of KsgA where loop 12 residues (UNP residues 164-172, UniProtKB-P37468 (RSMA_BACSU)) were exchanged with residues from ermC' protein (NTKR).
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: rsmA, ksgA, BSU00420 / Production host: Escherichia coli (E. coli)
References: UniProt: P37468, 16S rRNA (adenine1518-N6/adenine1519-N6)-dimethyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 2.71 Å3/Da / Density % sol: 54.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1M Sodium chloride, 0.05M Sodium cacodylate trihydrate pH 6.0, 10% w/v Polyethylene glycol 4000, 0.0005M Spermine

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.8→67.84 Å / Num. obs: 7342 / % possible obs: 99.8 % / Redundancy: 5.6 % / Rsym value: 0.185 / Net I/σ(I): 13.3
Reflection shellResolution: 3.8→3.897 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 5.57 / Rsym value: 0.539 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDSdata reduction
SCALAdata scaling
Auto-Rickshawphasing
RefinementResolution: 3.8→67.84 Å / Cor.coef. Fo:Fc: 0.88 / Cor.coef. Fo:Fc free: 0.81 / SU B: 64.354 / SU ML: 0.939 / Cross valid method: THROUGHOUT / ESU R Free: 1.04 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.38502 349 4.8 %RANDOM
Rwork0.30377 ---
obs0.30761 6971 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 61.524 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20 Å20 Å2
2--0.1 Å2-0 Å2
3----0.33 Å2
Refinement stepCycle: 1 / Resolution: 3.8→67.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3403 0 0 2 3405
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0193439
X-RAY DIFFRACTIONr_bond_other_d0.0020.023213
X-RAY DIFFRACTIONr_angle_refined_deg1.5711.9774698
X-RAY DIFFRACTIONr_angle_other_deg1.10337313
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.6725462
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.17625.045111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.56115491
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1441512
X-RAY DIFFRACTIONr_chiral_restr0.0820.2627
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213799
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02621
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_it3.3096.7361900
X-RAY DIFFRACTIONr_mcbond_other3.3086.7351901
X-RAY DIFFRACTIONr_mcangle_it5.6410.0862344
X-RAY DIFFRACTIONr_mcangle_other5.63910.0852345
X-RAY DIFFRACTIONr_scbond_it2.716.8821539
X-RAY DIFFRACTIONr_scbond_other2.7096.8811540
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.72710.2712355
X-RAY DIFFRACTIONr_long_range_B_refined9.04985.3033728
X-RAY DIFFRACTIONr_long_range_B_other9.04885.3033729
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 10888 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.14 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 3.799→3.897 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.445 23 -
Rwork0.346 494 -
obs--99.23 %

+
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