[English] 日本語
Yorodumi
- PDB-3skl: Crystal structure of the 2'- deoxyguanosine riboswitch bound to 2... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3skl
TitleCrystal structure of the 2'- deoxyguanosine riboswitch bound to 2'-deoxyguanosine, iridium hexammine soak
ComponentsRNA (66-MER)
KeywordsRNA / three way junction / riboswitch / deoxyguanosine
Function / homology2'-DEOXY-GUANOSINE / IRIDIUM HEXAMMINE ION / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9 Å
AuthorsPikovskaya, O. / Polonskaia, A. / Patel, D.J. / Serganov, A.
CitationJournal: Nat.Chem.Biol. / Year: 2011
Title: Structural principles of nucleoside selectivity in a 2'-deoxyguanosine riboswitch.
Authors: Pikovskaya, O. / Polonskaia, A. / Patel, D.J. / Serganov, A.
History
DepositionJun 22, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2011Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RNA (66-MER)
B: RNA (66-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,36120
Polymers42,7372
Non-polymers3,62418
Water905
1
A: RNA (66-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1328
Polymers21,3681
Non-polymers1,7647
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RNA (66-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,22912
Polymers21,3681
Non-polymers1,86111
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.002, 34.955, 111.057
Angle α, β, γ (deg.)90.00, 92.45, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-206-

MG

-
Components

#1: RNA chain RNA (66-MER)


Mass: 21368.484 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: dG riboswitch
#2: Chemical ChemComp-GNG / 2'-DEOXY-GUANOSINE


Mass: 267.241 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H13N5O4
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-IRI / IRIDIUM HEXAMMINE ION


Mass: 294.400 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: H18IrN6
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 2.22 Å3/Da / Density % sol: 44.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.05 M Na-HEPES, pH 7.5, ~40 % (v/v) pentaerythritol propoxylate, 0.2 M potassium chloride and 0.0-2.0 mM spermidine, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.1052 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 3, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1052 Å / Relative weight: 1
ReflectionResolution: 2.9→20 Å / Num. all: 8590 / Num. obs: 8487 / % possible obs: 98.8 % / Observed criterion σ(I): 3 / Redundancy: 6.5 % / Rmerge(I) obs: 0.102
Reflection shellResolution: 2.9→3 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.18 / Num. unique all: 764 / % possible all: 92.3

-
Processing

Software
NameVersionClassification
CBASSdata collection
PHENIXmodel building
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.9→20 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.926 / SU ML: 0.454 / Cross valid method: THROUGHOUT / ESU R Free: 0.467 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26371 405 4.7 %RANDOM
Rwork0.21863 ---
obs0.22079 8178 99.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Refinement stepCycle: LAST / Resolution: 2.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2826 114 5 2945
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0213264
X-RAY DIFFRACTIONr_angle_refined_deg1.00835124
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021382
X-RAY DIFFRACTIONr_nbd_refined0.170.21255
X-RAY DIFFRACTIONr_nbtor_refined0.280.21969
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.299
X-RAY DIFFRACTIONr_metal_ion_refined0.0110.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1830.233
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2250.24
LS refinement shellResolution: 2.9→2.974 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.476 22 -
Rwork0.306 551 -
obs--96.14 %

+
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