[English] 日本語
Yorodumi
- PDB-4xw0: Crystal structure of (GCCU(G-LNA)CCUGC)2 duplex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4xw0
TitleCrystal structure of (GCCU(G-LNA)CCUGC)2 duplex
ComponentsRNA (5'-R(*GP*CP*CP*UP*(LCG)P*CP*CP*UP*GP*C)-3')
KeywordsRNA / CCUG repeats / RNA duplex / Myotonic Dystrophy type 2 / tautomery / LNA residue / 3' overhanging nucleotides
Function / homologyRNA
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsKiliszek, A. / Banaszak, K. / Rypniewski, W.
Funding support Poland, 1items
OrganizationGrant numberCountry
National Science CentreUMO-2011/01/B/NZ1/04429 Poland
CitationJournal: Rna / Year: 2016
Title: Watson-Crick-like pairs in CCUG repeats: evidence for tautomeric shifts or protonation.
Authors: Rypniewski, W. / Banaszak, K. / Kulinski, T. / Kiliszek, A.
History
DepositionJan 28, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)6,4744
Polymers6,2822
Non-polymers1922
Water39622
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2190 Å2
ΔGint-24 kcal/mol
Surface area3790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)26.910, 26.910, 80.505
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

-
Components

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


Mass: 3140.910 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: RNA oligomer / Source: (synth.) Homo sapiens (human)
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 46.98 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: 40 mM magnesium sulphate, HEPES and 1.3 M lithium sulphate
PH range: 7

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 7, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.81→27 Å / Num. obs: 5249 / % possible obs: 99.6 % / Redundancy: 6.7 % / Biso Wilson estimate: 40.3 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 17.66
Reflection shellResolution: 1.81→1.92 Å / Redundancy: 6.6 % / Rmerge(I) obs: 1.355 / Mean I/σ(I) obs: 1.96 / % possible all: 99.1

-
Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GLP
Resolution: 1.81→26.91 Å / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 36.36 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.2984 524 10 %Random selection
Rwork0.2237 ---
obs0.2298 5239 99.43 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.3 Å2
Refinement stepCycle: LAST / Resolution: 1.81→26.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 397 10 22 429
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007478
X-RAY DIFFRACTIONf_angle_d1.497743
X-RAY DIFFRACTIONf_dihedral_angle_d13.957224
X-RAY DIFFRACTIONf_chiral_restr0.05196
X-RAY DIFFRACTIONf_plane_restr0.00820
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8066-1.98820.37121290.34951156X-RAY DIFFRACTION89
1.9882-2.27550.31891310.29621181X-RAY DIFFRACTION90
2.2755-2.86530.37861310.29811183X-RAY DIFFRACTION90
2.8653-190.25661330.17291189X-RAY DIFFRACTION89

+
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