[English] 日本語
Yorodumi
- PDB-1agz: THE SOLUTION NMR STRUCTURE OF AN (R)-A-(N6-ADENYL)-STYRENE OXIDE-... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1agz
TitleTHE SOLUTION NMR STRUCTURE OF AN (R)-A-(N6-ADENYL)-STYRENE OXIDE-RAS61 OLIGODEOXYNUCLEOTIDE MODIFIED AT THE THIRD POSITION OF THE CODON 61 REGION, MINIMIZED AVERAGE STRUCTURE
Components
  • DNA (5'-D(*CP*GP*GP*AP*CP*AP*RP*GP*AP*AP*G)-3')
  • DNA (5'-D(*CP*TP*TP*CP*TP*TP*GP*TP*CP*CP*G)-3')
KeywordsDNA / DNA DUPLEX / B-DNA / HUMAN N-RAS GENE / CODON 61 SEQUENCE / R-STYRENE OXIDE ADDUCT / N6-ADENINE / MAJOR GROOVE / DEOXYRIBONUCLEIC ACID
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / NOE-RESTRAINED MOLECULAR DYNAMICS, SIMULATED ANNEALING
AuthorsFeng, B. / Stone, M.P.
Citation
Journal: Biochemistry / Year: 1995
Title: Major groove (R)-alpha-(N6-adenyl)styrene oxide adducts in an oligodeoxynucleotide containing the human N-ras codon 61 sequence: conformations of the R(61,2) and R(61,3) sequence isomers from 1H NMR.
Authors: Feng, B. / Zhou, L. / Passarelli, M. / Harris, C.M. / Harris, T.M. / Stone, M.P.
#1: Journal: Chem.Res.Toxicol. / Year: 1995
Title: Solution Structure of an Oligodeoxynucleotide Containing the Human N-Ras Codon 61 Sequence Refined from 1H NMR Using Molecular Dynamics Restrained by Nuclear Overhauser Effects
Authors: Feng, B. / Stone, M.P.
History
DepositionMar 26, 1997Processing site: BNL
Revision 1.0Aug 20, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Feb 16, 2022Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Polymer sequence
Category: database_2 / entity_poly ...database_2 / entity_poly / pdbx_database_status / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_database_status.process_site / _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 2.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA (5'-D(*CP*GP*GP*AP*CP*AP*RP*GP*AP*AP*G)-3')
B: DNA (5'-D(*CP*TP*TP*CP*TP*TP*GP*TP*CP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)6,8282
Polymers6,8282
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 1THIS STRUCTURE PROVIDED THE BEST-FIT FOR THE NOE DATA BASED ON THE RELAXATION MATRIX ANALYSIS USING CORMA
Representative

-
Components

#1: DNA chain DNA (5'-D(*CP*GP*GP*AP*CP*AP*RP*GP*AP*AP*G)-3')


Mass: 3536.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: (R)-(N6-ADENYL)-STYRENE OXIDE-RAS61-3 DNA ADDUCT
#2: DNA chain DNA (5'-D(*CP*TP*TP*CP*TP*TP*GP*TP*CP*CP*G)-3')


Mass: 3291.145 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: (R)-(N6-ADENYL)-STYRENE OXIDE-RAS61-3 DNA ADDUCT

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
1212QF-COSY
131AND TOCSY
141: NOESY
1512QF-COSY
161AND(DO
17105'-D

-
Sample preparation

Sample conditionspH: 6.9 / Temperature: 293 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometerType: Bruker AMX500 / Manufacturer: Bruker / Model: AMX500 / Field strength: 500 MHz

-
Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
Felixstructure solution
X-PLORstructure solution
MARDIGRASstructure solution
CORMAstructure solution
RefinementMethod: NOE-RESTRAINED MOLECULAR DYNAMICS, SIMULATED ANNEALING
Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE.
NMR ensembleConformer selection criteria: THIS STRUCTURE PROVIDED THE BEST-FIT FOR THE NOE DATA BASED ON THE RELAXATION MATRIX ANALYSIS USING CORMA
Conformers calculated total number: 1 / Conformers submitted total number: 1

+
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