[English] 日本語
Yorodumi
- PDB-2m57: NMR solution structure of domain 5 from Azotobacter vinelandii In... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2m57
TitleNMR solution structure of domain 5 from Azotobacter vinelandii Intron 5 at pH 7.8
ComponentsRNA_(35-MER)
KeywordsRNA / ribozyme / group II intron / hairpin
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesAzotobacter vinelandii (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model1
AuthorsPechlaner, M. / Donghi, D. / Zelenay, V. / Sigel, R.K.O.
CitationJournal: To be Published
Title: Acid-base equilibria near neutral pH in the catalytic triad and the bulge of domain 5 of a bacterial group II intron
Authors: Pechlaner, M. / Donghi, D. / Zelenay, V. / Sigel, R.K.O.
History
DepositionFeb 15, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 26, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RNA_(35-MER)


Theoretical massNumber of molelcules
Total (without water)11,2691
Polymers11,2691
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: RNA chain RNA_(35-MER)


Mass: 11268.708 Da / Num. of mol.: 1 / Fragment: group II intron Domain 5 (D5) / Source method: obtained synthetically
Details: the sequence occurs naturally as part of Intron 5 from A.vinelandii and was transcribed in vitro using T7 RNA polymerase from a dsDNA template
Source: (synth.) Azotobacter vinelandii (bacteria)

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
1252D 1H-1H NOESY
2322D 1H-1H NOESY
1412D 1H-1H TOCSY
2542D 1H-15N HSQC
1632D 1H-13C HSQC aromatic
1732D 1H-13C HSQC aliphatic
2842D JNN HNN COSY
3912D 1H-1H NOESY
41012D 1H-1H NOESY
51122D 1H-1H NOESY
61222D 1H-1H NOESY
31332D 1H-13C HSQC aromatic
41432D 1H-13C HSQC aromatic
41532D 1H-13C HSQC aliphatic
51642D 1H-15N HSQC
61742D 1H-15N HSQC
51842D JNN HNN COSY
61942D JNN HNN COSY

-
Sample preparation

Details
Solution-IDContentsSolvent system
10.5-1 mM RNA (35-MER), 60 mM potassium chloride, 10 uM EDTA, 100% D2O100% D2O
20.5-1 mM RNA (35-MER), 60 mM potassium chloride, 10 uM EDTA, 90% H2O/10% D2O90% H2O/10% D2O
30.5-1 mM [100% 13C; 100% 15N] RNA (35-MER), 60 mM potassium chloride, 10 uM EDTA, 100% D2O100% D2O
40.5-1 mM [100% 13C; 100% 15N] RNA (35-MER), 60 mM potassium chloride, 10 uM EDTA, 90% H2O/10% D2O90% H2O/10% D2O
50.5-1 mM [3',4',5',5'',5]-100% 2D RNA (35-MER), 60 mM potassium chloride, 10 uM EDTA, 100% D2O100% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMRNA (35-MER)-10.5-11
60 mMpotassium chloride-21
10 uMEDTA-31
mMRNA (35-MER)-40.5-12
60 mMpotassium chloride-52
10 uMEDTA-62
mMRNA (35-MER)-7[100% 13C; 100% 15N]0.5-13
60 mMpotassium chloride-83
10 uMEDTA-93
mMRNA (35-MER)-10[100% 13C; 100% 15N]0.5-14
60 mMpotassium chloride-114
10 uMEDTA-124
mMRNA (35-MER)-13[3',4',5',5'',5]-100% 2D0.5-15
60 mMpotassium chloride-145
10 uMEDTA-155
Sample conditions
Conditions-IDIonic strengthPressure (kPa)Temperature (K)pH
160ambient 300 K
260ambient 275 K7.8
560ambient 275 K5.2
660ambient 275 K6.7

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE7001
Bruker AvanceBrukerAVANCE6002
Bruker AvanceBrukerAVANCE5003

-
Processing

NMR software
NameVersionDeveloperClassification
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
X-PLOR NIH2.3Schwieters, Kuszewski, Tjandra and Clorerefinement
X-PLOR NIH2.3Schwieters, Kuszewski, Tjandra and Clorestructure solution
MOLMOLKoradi, Billeter and Wuthrichdata analysis
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
SparkyGoddarddata analysis
TopSpin3.0.aBruker Biospinprocessing
TopSpin3.0.aBruker Biospindata analysis
CurvesLaverydata analysis
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 660 / NOE intraresidue total count: 238 / NOE long range total count: 98 / NOE medium range total count: 14 / NOE sequential total count: 310 / Hydrogen bond constraints total count: 56
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0.2 Å / Maximum upper distance constraint violation: 0.2 Å

+
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