[English] 日本語
Yorodumi
- PDB-7eem: RNA bulged-G motif -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7eem
TitleRNA bulged-G motif
ComponentsRNA (27-MER)
KeywordsRNA / Bulged-G motif
Function / homology: / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.593 Å
AuthorsKondo, J. / Sekiguchi, S.
CitationJournal: To Be Published
Title: RNA bulged-G motif
Authors: Kondo, J. / Sekiguchi, S.
History
DepositionMar 19, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 23, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RNA (27-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,8987
Polymers8,7441
Non-polymers1,1536
Water724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-6 kcal/mol
Surface area4580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)25.132, 53.316, 105.639
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

-
Components

#1: RNA chain RNA (27-MER)


Mass: 8744.255 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-IR / IRIDIUM ION


Mass: 192.217 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ir
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.02 Å3/Da / Density % sol: 39.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: sodium cacodylate, MPD, hexammine cobalt, potassium chloride

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1.10567 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.10567 Å / Relative weight: 1
ReflectionResolution: 2.59→26.658 Å / Num. obs: 4239 / % possible obs: 99.1 % / Redundancy: 3.397 % / Biso Wilson estimate: 34.87 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.089 / Rrim(I) all: 0.106 / Χ2: 1.747 / Net I/σ(I): 10.87
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.59-2.663.1940.3743.9710543423300.8940.44896.5
2.66-2.733.3690.2785.139872962930.8950.33399
2.73-2.813.4530.2426.0410292982980.9410.288100
2.81-2.93.2950.2136.189492882880.9550.257100
2.9-2.993.1170.1587.638792832820.970.19199.6
2.99-3.13.2480.1448.978772702700.9770.172100
3.1-3.223.4290.10310.088642572520.9880.12498.1
3.22-3.353.5840.09411.439212572570.9920.111100
3.35-3.53.6550.08512.538702392380.9930.199.6
3.5-3.673.5720.08312.838682452430.990.09999.2
3.67-3.873.6080.08114.617362052040.9920.09599.5
3.87-4.13.4430.08414.627232112100.9850.199.5
4.1-4.383.440.08215.226571931910.9840.09899
4.38-4.733.4480.06715.296241821810.9930.07999.5
4.73-5.193.3580.06516.235911771760.9890.07799.4
5.19-5.83.0270.0715.714481541480.9850.08496.1
5.8-6.73.3150.05516.434211271270.9910.065100
6.7-8.23.670.05717.874111121120.9930.066100
8.2-11.63.6070.05218.2132189890.9940.061100
11.6-26.6583.3620.03118.415848470.9980.03897.9

-
Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.17.1refinement
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Q9A

1q9a


Resolution: 2.593→26.658 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.42 / Phase error: 28.48 / Stereochemistry target values: ML
Details: The Sf file contains friedel pairs under F_plus and F_minus columns.
RfactorNum. reflection% reflection
Rfree0.2435 417 9.84 %
Rwork0.1796 3822 -
obs0.1861 4239 99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 228.25 Å2 / Biso mean: 24.1093 Å2 / Biso min: 5.14 Å2
Refinement stepCycle: final / Resolution: 2.593→26.658 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 556 6 4 566
Biso mean--129.21 23.01 -
Num. residues----26
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005622
X-RAY DIFFRACTIONf_angle_d0.934969
X-RAY DIFFRACTIONf_chiral_restr0.038129
X-RAY DIFFRACTIONf_plane_restr0.00626
X-RAY DIFFRACTIONf_dihedral_angle_d13.463308
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 99 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.593-2.96750.36341400.26991286
2.9675-3.73710.21891440.15681256
3.7371-26.6580.21271330.16141280

+
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