[English] 日本語
Yorodumi
- PDB-4e59: Crystal structure of GCCGCCGC duplex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4.0E+59
TitleCrystal structure of GCCGCCGC duplex
ComponentsRNA duplex containing CCG repeats
KeywordsRNA / 3' slippery duplexes / X-linked mental retardation / Huntington's disease / myotonic dystrophy type 1 / CCG repeats
Function / homologyRNA
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å
AuthorsKiliszek, A. / Kierzek, R. / Krzyzosiak, W.J. / Rypniewski, W.
CitationJournal: Nucleic Acids Res. / Year: 2012
Title: Crystallographic characterization of CCG repeats.
Authors: Kiliszek, A. / Kierzek, R. / Krzyzosiak, W.J. / Rypniewski, W.
History
DepositionMar 14, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Source and taxonomy / Category: pdbx_entity_src_syn / software
Item: _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific / _software.name
Revision 1.2Sep 13, 2023Group: 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 duplex containing CCG repeats
B: RNA duplex containing CCG repeats


Theoretical massNumber of molelcules
Total (without water)5,0332
Polymers5,0332
Non-polymers00
Water28816
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area570 Å2
ΔGint-4 kcal/mol
Surface area3060 Å2
MethodPISA
2
A: RNA duplex containing CCG repeats
B: RNA duplex containing CCG repeats

A: RNA duplex containing CCG repeats
B: RNA duplex containing CCG repeats

A: RNA duplex containing CCG repeats
B: RNA duplex containing CCG repeats


Theoretical massNumber of molelcules
Total (without water)15,0996
Polymers15,0996
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area3640 Å2
ΔGint-46 kcal/mol
Surface area7280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.580, 40.580, 56.144
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-105-

HOH

21A-106-

HOH

31B-105-

HOH

41B-106-

HOH

-
Components

#1: RNA chain RNA duplex containing CCG repeats


Mass: 2516.569 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: This sequence is a part of mRNA in humans / Source: (synth.) Homo sapiens (human)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 1.77 Å3/Da / Density % sol: 30.41 %
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: magnesium acetate, MES and ammonium sulphate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 303K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 5, 2010
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.54→20 Å / Num. all: 5101 / Num. obs: 5101 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Rsym value: 0.04 / Net I/σ(I): 26.14
Reflection shellResolution: 1.54→1.57 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 2.06 / Num. unique all: 262 / Rsym value: 0.711 / % possible all: 100

-
Processing

Software
NameVersionClassification
MAR345data collection
PHASERphasing
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Starting model: 4.0E+58 / Resolution: 1.54→18.715 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 30.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3035 501 100 %RANDOM
Rwork0.2553 ---
all0.257 5073 --
obs0.2553 5073 99.41 %-
Solvent computationShrinkage radii: 0.16 Å / VDW probe radii: 0.5 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 63.918 Å2 / ksol: 0.458 e/Å3
Displacement parametersBiso mean: 27.79 Å2
Baniso -1Baniso -2Baniso -3
1-4.8628 Å20 Å2-0 Å2
2--4.8628 Å2-0 Å2
3----9.7256 Å2
Refinement stepCycle: LAST / Resolution: 1.54→18.715 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 300 0 16 316
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01332
X-RAY DIFFRACTIONf_angle_d1.29516
X-RAY DIFFRACTIONf_dihedral_angle_d13.993164
X-RAY DIFFRACTIONf_chiral_restr0.07670
X-RAY DIFFRACTIONf_plane_restr0.01514
LS refinement shellResolution: 1.54→1.695 Å
RfactorNum. reflection% reflection
Rfree0.3627 130 -
Rwork0.3411 161 -
obs-1270 100 %

+
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