[English] 日本語
Yorodumi
- PDB-6xur: RNA dodecamer with a 6-hydrazino-2-aminopurine modified base -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6xur
TitleRNA dodecamer with a 6-hydrazino-2-aminopurine modified base
ComponentsRNA dodecamer with a 6-hydrazino-2-aminopurine modified base
KeywordsRNA / 6-hydrazino-2-aminopurine modified base
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsEnnifar, E. / Micura, R. / Gasser, C. / Brillet, K.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2020
Title: Thioguanosine Conversion Enables mRNA-Lifetime Evaluation by RNA Sequencing Using Double Metabolic Labeling (TUC-seq DUAL).
Authors: Gasser, C. / Delazer, I. / Neuner, E. / Pascher, K. / Brillet, K. / Klotz, S. / Trixl, L. / Himmelstoss, M. / Ennifar, E. / Rieder, D. / Lusser, A. / Micura, R.
History
DepositionJan 21, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 19, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2020Group: Database references / Category: citation / Item: _citation.title
Revision 1.2Apr 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3May 5, 2021Group: Derived calculations / Source and taxonomy
Category: pdbx_entity_src_syn / pdbx_struct_conn_angle / struct_conn
Item: _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific ..._pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific / _pdbx_entity_src_syn.pdbx_beg_seq_num / _pdbx_entity_src_syn.pdbx_end_seq_num / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id
Revision 1.4Jan 24, 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 dodecamer with a 6-hydrazino-2-aminopurine modified base
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,9303
Polymers3,8811
Non-polymers492
Water1,38777
1
A: RNA dodecamer with a 6-hydrazino-2-aminopurine modified base
hetero molecules

A: RNA dodecamer with a 6-hydrazino-2-aminopurine modified base
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,8606
Polymers7,7632
Non-polymers974
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area1530 Å2
ΔGint-23 kcal/mol
Surface area4520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.420, 35.030, 32.030
Angle α, β, γ (deg.)90.000, 129.724, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-1235-

HOH

-
Components

#1: RNA chain RNA dodecamer with a 6-hydrazino-2-aminopurine modified base


Mass: 3881.390 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: 6HA = 6-hydrazino-2-aminopurine / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: MPD, sodium cacodylate, spermine tetrahydrochloride, NaCl, MgCl2

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1→50 Å / Num. obs: 113052 / % possible obs: 97.1 % / Redundancy: 6 % / Biso Wilson estimate: 14.43 Å2 / CC1/2: 0.999 / Net I/σ(I): 9.66
Reflection shellResolution: 1→1.03 Å / Num. unique obs: 3237 / CC1/2: 0.0056 / % possible all: 76.1

-
Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PHENIX1.15.2_3472refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Q1R

2q1r


Resolution: 1.1→24.64 Å / SU ML: 0.178 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 24.6426
RfactorNum. reflection% reflection
Rfree0.1803 717 4.99 %
Rwork0.1538 --
obs0.1551 14367 99.78 %
Solvent computationShrinkage radii: 0.3 Å / VDW probe radii: 0.6 Å
Displacement parametersBiso mean: 19.47 Å2
Refinement stepCycle: LAST / Resolution: 1.1→24.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 257 2 77 336
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122287
X-RAY DIFFRACTIONf_angle_d1.9781446
X-RAY DIFFRACTIONf_chiral_restr0.046958
X-RAY DIFFRACTIONf_plane_restr0.045213
X-RAY DIFFRACTIONf_dihedral_angle_d6.5717131
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1-1.180.30871430.3152707X-RAY DIFFRACTION99.44
1.18-1.30.22771430.19052703X-RAY DIFFRACTION99.86
1.3-1.490.22111430.15832724X-RAY DIFFRACTION99.97
1.49-1.880.17311430.1462743X-RAY DIFFRACTION99.86
1.88-24.640.16381450.14312773X-RAY DIFFRACTION99.79

+
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