[English] 日本語
Yorodumi
- PDB-2be0: Complex Between Paromomycin Derivative JS5-39 and the 16S-Rrna A-Site. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2be0
TitleComplex Between Paromomycin Derivative JS5-39 and the 16S-Rrna A-Site.
Components5'-R(*CP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*C)-3'
KeywordsRNA/antibiotic / RNA-AMINOGLYCOSIDE INTERACTIONS / A SITE / UOU PAIRS / AA BULGES / RNA-antibiotic complex
Function / homologyChem-JS5 / RNA / RNA (> 10)
Function and homology information
Biological speciesStreptomyces rimosus subsp. paromomycinus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.63 Å
AuthorsFrancois, B. / Westhof, E.
CitationJournal: ANGEW.CHEM.INT.ED.ENGL. / Year: 2004
Title: Antibacterial aminoglycosides with a modified mode of binding to the ribosomal-RNA decoding site
Authors: Francois, B. / Szychowski, J. / Adhikari, S.S. / Pachamuthu, K. / Swayze, E.E. / Griffey, R.H. / Migawa, M.T. / Westhof, E. / Hanessian, S.
History
DepositionOct 21, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 20, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Database references / Derived calculations / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / entity / pdbx_entity_nonpoly / pdbx_molecule_features / struct_site
Item: _chem_comp.name / _chem_comp.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Mar 13, 2024Group: Source and taxonomy / Category: pdbx_entity_src_syn / Item: _pdbx_entity_src_syn.entity_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 5'-R(*CP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*C)-3'
B: 5'-R(*CP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6084
Polymers14,0972
Non-polymers1,5122
Water79344
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.141, 39.141, 99.140
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41
DetailsThe biological assembly is the duplex

-
Components

#1: RNA chain 5'-R(*CP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*C)-3'


Mass: 7048.259 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: 16S Rrna A Site
Source: (synth.) Streptomyces rimosus subsp. paromomycinus (bacteria)
#2: Chemical ChemComp-JS5 / (2S,3S,4R,5R,6R)-5-AMINO-2-(AMINOMETHYL)-6-((2R,3R,4R,5S)-5-((1R,2R,3S,5R,6S)-3,5-DIAMINO-2-((2S,3R,4R,5S,6R)-3-AMINO-4 ,5-DIHYDROXY-6-(HYDROXYMETHYL)-TETRAHYDRO-2H-PYRAN-2-YLOXY)-6-HYDROXYCYCLOHEXYLOXY)-2-(HYDROXYMETHYL)-4-(2-((R)-PIPERIDI N-3-YLMETHYLAMINO)ETHOXY)-TETRAHYDROFURAN-3-YLOXY)-TETRAHYDRO-2H-PYRAN-3,4-DIOL / 2"-O-[N-(3-(AMINOMETHYL)-PYRIDINE)-2-AMINOETHYL]PAROMOMYCIN / O-2-AMINO-2-DEOXY-ALPHA-D-GLUCOPYRANOSYL-(1,4)-O-[O-2,6-DIAMINO-2,6-DIDEOXY-BETA-L-IDOPYRANOSYL-(1,3)-BETA-D-2-O-(3-ETHY LAMINOMETHYL)-PYRIDYL-(1,5)]-2-DEOXY-D-STREPTAMINE


Mass: 755.855 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H61N7O14
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 2.69 Å3/Da / Density % sol: 54.34 %
Crystal growTemperature: 310 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 6% MPD, 0.3M potassium chloride, 5% glycerol, 0.1M cacodylate, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 310K
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2potassium chloride11
3glycerol11
4cacodylate11
5H2O11
6MPD12
7potassium chloride12
8cacodylate12
9H2O12

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 13, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.63→50 Å / Num. all: 46641 / Num. obs: 46641 / % possible obs: 99 % / Observed criterion σ(I): 5 / Redundancy: 10 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 28
Reflection shellResolution: 2.63→2.72 Å / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 9.4 / % possible all: 100

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1J7T

1j7t


Resolution: 2.63→30 Å / σ(F): 2
Details: G. PARKINSON, J. VOJTECHOVSKY, L. CLOWNEY,A.T. BRUNGER, H.M. BERMAN, NEW PARAMETERS FOR THE REFINEMENT OF NUCLEIC ACID CONTAINING STRUCTURES, ACTA CRYST. D, 52, 57-64 (1996)
RfactorNum. reflectionSelection details
Rfree0.2665 3842 RANDOM
Rwork0.2236 --
all-4453 -
obs-4291 -
Refine analyzeLuzzati coordinate error obs: 0.42 Å / Luzzati sigma a obs: 0.52 Å
Refinement stepCycle: LAST / Resolution: 2.63→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 898 104 44 1046
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_d1.023
X-RAY DIFFRACTIONc_dihedral_angle_d10.251
X-RAY DIFFRACTIONc_improper_angle_d1.241
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1dna-rna_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param
X-RAY DIFFRACTION4JS5_39.param

+
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