[English] 日本語
Yorodumi
- PDB-7ei5: GNRA tetraloop receptor motif composed of RNA and DNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ei5
TitleGNRA tetraloop receptor motif composed of RNA and DNA
ComponentsDNA/RNA (35-MER)
KeywordsDNA-RNA HYBRID / GNRA tetraloop / tetraloop receptor
Function / homology: / STRONTIUM ION / DNA/RNA hybrid / DNA/RNA hybrid (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsKondo, J. / Hayasaka, A.
CitationJournal: To Be Published
Title: RNA GNRA tetraloop and tetraloop receptor motifs
Authors: Kondo, J. / Hayasaka, A.
History
DepositionMar 30, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 30, 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: DNA/RNA (35-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,65019
Polymers11,1301
Non-polymers1,52018
Water181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint-29 kcal/mol
Surface area6170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.220, 83.220, 67.164
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

-
Components

#1: DNA/RNA hybrid DNA/RNA (35-MER)


Mass: 11129.910 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#3: Chemical
ChemComp-SR / STRONTIUM ION


Mass: 87.620 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Sr
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 3.96 Å3/Da / Density % sol: 68.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: sodium cacodylate, MPD, hexammine cobalt, strontium chloride

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Jun 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→30.44 Å / Num. obs: 7623 / % possible obs: 98.8 % / Redundancy: 2.669 % / Biso Wilson estimate: 37.566 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.063 / Rrim(I) all: 0.079 / Χ2: 1.057 / Net I/σ(I): 13.75 / Num. measured all: 20349 / Scaling rejects: 2
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
2.9-2.972.4310.2863.313815985680.8720.36695
2.97-3.062.5770.2064.5113455265220.9530.26199.2
3.06-3.142.7890.137.3715705665630.9780.16199.5
3.14-3.242.7510.1028.5913594944940.9890.127100
3.24-3.352.7650.0919.5814685385310.990.11398.7
3.35-3.462.7480.1049.2312864704680.9850.12999.6
3.46-3.62.7440.07511.1413174824800.9940.09399.6
3.6-3.742.7440.0712.0812214504450.9940.08898.9
3.74-3.912.7240.06913.511934384380.9910.086100
3.91-4.12.6720.05415.6411654364360.9940.068100
4.1-4.322.6840.05317.2710013783730.9940.06798.7
4.32-4.582.5530.04517.999833883850.9950.05699.2
4.58-4.92.5680.04220.088683483380.9950.05297.1
4.9-5.292.3690.03621.757963463360.9950.04697.1
5.29-5.82.5510.03423.617322882870.9970.04399.7
5.8-6.482.610.03123.677102742720.9980.03999.3
6.48-7.482.9120.03525.997252502490.9980.04399.6
7.48-9.172.8870.03627.015862042030.9960.04499.5
9.17-12.962.8310.03828.244531601600.9960.047100
12.96-30.442.5330.03729.3719080750.9980.04993.8

-
Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.17.1refinement
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4fnj

4fnj


Resolution: 2.9→30.44 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 22.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1992 745 9.78 %
Rwork0.1721 6874 -
obs0.1748 7619 98.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 143.69 Å2 / Biso mean: 35.5645 Å2 / Biso min: 11.34 Å2
Refinement stepCycle: final / Resolution: 2.9→30.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 738 19 1 758
Biso mean--101.51 11.34 -
Num. residues----35
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9-3.120.31111450.26261374151998
3.12-3.440.23551460.1821391153799
3.44-3.930.18071580.16651348150699
3.93-4.950.17911520.141381153399
4.96-30.440.17261440.16391380152499

+
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