[English] 日本語
Yorodumi
- PDB-1qyr: 2.1 Angstrom Crystal structure of KsgA: A Universally Conserved A... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1qyr
Title2.1 Angstrom Crystal structure of KsgA: A Universally Conserved Adenosine Dimethyltransferase
ComponentsHigh level Kasugamycin resistance protein
KeywordsTRANSFERASE / TRANSLATION / Kasugamycin resistance / adenosine dimethyltransferase / rRNA modification
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 base methylation / rRNA methylation / ribosomal small subunit binding / maturation of SSU-rRNA / rRNA processing / ribosomal small subunit assembly / double-stranded DNA binding ...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 base methylation / rRNA methylation / ribosomal small subunit binding / maturation of SSU-rRNA / rRNA processing / ribosomal small subunit assembly / double-stranded DNA binding / response to antibiotic / mRNA 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 speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SIRAS / Resolution: 2.1 Å
AuthorsO'Farrell, H.C. / Scarsdale, J.N. / Wright, H.T. / Rife, J.P.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Crystal structure of KsgA, a universally conserved rRNA adenine dimethyltransferase in Escherichia coli
Authors: O'Farrell, H.C. / Scarsdale, J.N. / Rife, J.P.
History
DepositionSep 11, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: High level Kasugamycin resistance protein
B: High level Kasugamycin resistance protein


Theoretical massNumber of molelcules
Total (without water)55,9772
Polymers55,9772
Non-polymers00
Water4,252236
1
A: High level Kasugamycin resistance protein


Theoretical massNumber of molelcules
Total (without water)27,9881
Polymers27,9881
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: High level Kasugamycin resistance protein


Theoretical massNumber of molelcules
Total (without water)27,9881
Polymers27,9881
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)173.912, 38.428, 82.982
Angle α, β, γ (deg.)90.00, 90.005, 90.00
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121
DetailsThe Biological assembly is one monomer. The assymetric unit contains two monomers

-
Components

#1: Protein High level Kasugamycin resistance protein / E.C.2.1.1.- / KsgA / Dimethyladenosine transferase / S-adenosylmethionine-6-N' / N'-adenosyl(rRNA) ...KsgA / Dimethyladenosine transferase / S-adenosylmethionine-6-N' / N'-adenosyl(rRNA) dimethyltransferase / 16S rRNA dimethylase / Kasugamycin dimethyltransferase


Mass: 27988.273 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ksgA / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174
References: UniProt: P06992, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / 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: 2.41 Å3/Da / Density % sol: 48.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: PEG 4000, 0.2M calcium acetate, 50mM TRIS, pH 7.4, 50 mM NH4Cl, 6mM B-mercaptoethanol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 98 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Mar 21, 2003 / Details: Osmic confocal optics
RadiationMonochromator: Osmic Confocal Optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→40 Å / Num. all: 33939 / Num. obs: 32474 / % possible obs: 95.6 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 42 Å2 / Rsym value: 0.08 / Net I/σ(I): 17.2
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 2.7 / Num. unique all: 1647 / Rsym value: 0.328 / % possible all: 76.6

-
Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
SCALEPACKdata scaling
SHARPphasing
CNS1refinement
DENZOdata reduction
RefinementMethod to determine structure: SIRAS / Resolution: 2.1→40 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.93 / SU B: 5.157 / SU ML: 0.137 / TLS residual ADP flag: LIKELY RESIDUAL
Isotropic thermal model: TLS + Individual Isotropic B factors
Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.245 / ESU R Free: 0.2 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: Refined also by CNS 1. The same test set was used in both CNS and REFMAC
RfactorNum. reflection% reflectionSelection details
Rfree0.23802 3159 10 %random
Rwork0.18901 ---
all0.19378 32656 --
obs0.19377 28356 96.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 27.326 Å2
Baniso -1Baniso -2Baniso -3
1--1.21 Å20 Å21.05 Å2
2--1.94 Å20 Å2
3----0.73 Å2
Refine analyzeLuzzati coordinate error obs: 0.263 Å / Luzzati d res low obs: 8 Å
Refinement stepCycle: LAST / Resolution: 2.1→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3876 0 0 236 4112
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223960
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3521.9635395
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.315502
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_chiral_restr0.090.2626
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023024
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2080.21826
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.2244
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2210.256
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1260.216
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.7141.52532
X-RAY DIFFRACTIONr_mcangle_it1.31524105
X-RAY DIFFRACTIONr_scbond_it2.28431428
X-RAY DIFFRACTIONr_scangle_it3.6664.51290
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.279 209
Rwork0.218 1829
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)
10.94810.059-0.03950.3725-0.36191.7122-0.0245-0.05760.0560.0469-0.0706-0.0458-0.0805-0.00120.0950.0659-0.0041-0.03710.0642-0.00350.030545.533725.562520.5766
22.9461-0.105-1.31340.72-0.72132.56060.0104-0.21060.0303-0.0451-0.148-0.1833-0.12590.37950.13760.0487-0.009100.11580.05560.047162.915533.2071-5.1564
31.62310.4465-0.75270.51010.18130.8494-0.0725-0.0773-0.10420.0305-0.0108-0.0364-0.0120.04030.08330.05640.0085-0.01170.0013-0.00180.0869103.947841.8075-39.1212
46.33081.1531-3.38291.3317-1.63334.7289-0.4713-0.561-0.70720.16650.0644-0.19940.24810.41790.40690.10110.05660.08930.09880.06740.139282.445529.4999-19.4404
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA17 - 1951 - 179
2X-RAY DIFFRACTION2AA203 - 268187 - 252
3X-RAY DIFFRACTION3BB17 - 1951 - 179
4X-RAY DIFFRACTION4BB203 - 268187 - 252

+
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://pdbjlvh1.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