[English] 日本語
Yorodumi
- PDB-1bps: MINOR CONFORMER OF A BENZO[A]PYRENE DIOL EPOXIDE ADDUCT OF DA IN ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1bps
TitleMINOR CONFORMER OF A BENZO[A]PYRENE DIOL EPOXIDE ADDUCT OF DA IN DUPLEX DNA
Components
  • DNA (5'-D(*CP*TP*CP*GP*GP*GP*AP*CP*C)-3')
  • DNA (5'-D(*GP*GP*TP*CP*(BAP)AP*CP*GP*AP*G)-3')
KeywordsDNA / DEOXYRIBONUCLEIC ACID / BENZO[A]PYRENE DIOL EPOXIDE ADDUCT / DUPLEX DNA
Function / homology1,2,3-TRIHYDROXY-1,2,3,4-TETRAHYDROBENZO[A]PYRENE / DNA
Function and homology information
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / RELAXATION MATRIX REFINEMENT OF NOE DISTANCE RESTRAINTS, RESTRAINED MOLECULAR DYNAMICS WITH SIMULATED ANNEALING
AuthorsSchwartz, J.S. / Rice, J.S. / Luxon, B.A. / Sayer, J.M. / Xie, G. / Yeh, H.J.C. / Liu, X. / Jerina, D.M. / Gorenstein, D.G.
CitationJournal: Biochemistry / Year: 1997
Title: Solution structure of the minor conformer of a DNA duplex containing a dG mismatch opposite a benzo[a]pyrene diol epoxide/dA adduct: glycosidic rotation from syn to anti at the modified deoxyadenosine.
Authors: Schwartz, J.L. / Rice, J.S. / Luxon, B.A. / Sayer, J.M. / Xie, G. / Yeh, H.J. / Liu, X. / Jerina, D.M. / Gorenstein, D.G.
History
DepositionAug 6, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Aug 19, 1998Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy
Category: database_2 / pdbx_entity_src_syn ...database_2 / pdbx_entity_src_syn / pdbx_nmr_exptl / pdbx_nmr_representative / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_exptl.type / _pdbx_nmr_software.authors / _pdbx_nmr_software.classification / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA (5'-D(*GP*GP*TP*CP*(BAP)AP*CP*GP*AP*G)-3')
B: DNA (5'-D(*CP*TP*CP*GP*GP*GP*AP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,8023
Polymers5,4982
Non-polymers3041
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 1
RepresentativeModel #1minimized average structure

-
Components

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


Mass: 2780.836 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: (+)-(7R,8S,9S,10R)-7,8-DIHYDROXY-9,10-EPOXY-7,8,9,10- TETRAHYDROBENZO[A]PYRENE IS COVALENTLY BONDED TO THE EXOCYCLIC N6 AMINO GROUP OF DEOXYADENOSINE IN THE CENTER OF THE DUPLEX THROUGH ...Details: (+)-(7R,8S,9S,10R)-7,8-DIHYDROXY-9,10-EPOXY-7,8,9,10- TETRAHYDROBENZO[A]PYRENE IS COVALENTLY BONDED TO THE EXOCYCLIC N6 AMINO GROUP OF DEOXYADENOSINE IN THE CENTER OF THE DUPLEX THROUGH TRANS ADDITION AT THE C10 OF THE EPOXIDE.
Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(*CP*TP*CP*GP*GP*GP*AP*CP*C)-3')


Mass: 2716.787 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: BENZO[A]PYRENE DIOL EPOXIDE ADDUCT OF DA / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-BAP / 1,2,3-TRIHYDROXY-1,2,3,4-TETRAHYDROBENZO[A]PYRENE


Mass: 304.339 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H16O3

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121ROESY
131TOCSY
1412D EXCHANGE-ONLY SPECTRA
NMR detailsText: MINIMIZED AVERAGE STRUCTURE. THE STRUCTURE WAS DETERMINED USING DISTANCE RESTRAINTS DERIVED FROM 2D NOESY EXPERIMENTS DONE IN 99.999% D2O AND 90% H2O/ 10% D2O. 2D ROESY, TOCSY, AND EXCHANGE- ...Text: MINIMIZED AVERAGE STRUCTURE. THE STRUCTURE WAS DETERMINED USING DISTANCE RESTRAINTS DERIVED FROM 2D NOESY EXPERIMENTS DONE IN 99.999% D2O AND 90% H2O/ 10% D2O. 2D ROESY, TOCSY, AND EXCHANGE-ONLY EXPERIMENTS WERE USED IN THE CHEMICAL SHIFT ASSIGNMENT PROCESS.

-
Sample preparation

Sample conditionsIonic strength: 76 mM / pH: 6.8 / Pressure: 1 atm / Temperature: 288 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITYPLUSVarianUNITYPLUS7501
Varian UNITYPLUSVarianUNITYPLUS6002

-
Processing

NMR software
NameVersionDeveloperClassification
Amber4.1PEARLMAN,CASE,CALDWELL,ROSS,CHEATHAM, FERGUSON,SEIBEL,SINGH,WEINER,KOLLMANrefinement
MORASS2.2Luxonstructure calculation
Amber4.1PEARLMAN,CASE,CALDWELL,ROSS,CHEATHAM, FERGUSON,SEIBEL,SINGH,WEINER,KOLLMANstructure calculation
RefinementMethod: RELAXATION MATRIX REFINEMENT OF NOE DISTANCE RESTRAINTS, RESTRAINED MOLECULAR DYNAMICS WITH SIMULATED ANNEALING
Software ordinal: 1
Details: THE FOLLOWING RESTRAINTS WERE APPLIED IN THE MOLECULAR DYNAMICS/ENERGY MINIMIZATION CALCULATIONS: (1) INTER-PROTON DISTANCE RESTRAINTS DIRECTLY DERIVED FROM RELAXATION MATRIX ANALYSIS OF NOE ...Details: THE FOLLOWING RESTRAINTS WERE APPLIED IN THE MOLECULAR DYNAMICS/ENERGY MINIMIZATION CALCULATIONS: (1) INTER-PROTON DISTANCE RESTRAINTS DIRECTLY DERIVED FROM RELAXATION MATRIX ANALYSIS OF NOE DATA; (2) IMINO PROTON HYDROGEN BOND RESTRAINTS FOR ALL BASE PAIRS EXCEPT THE CENTRAL DA-DG MISMATCH PAIR. THE MODIFIED DA RESIDUE OF THIS MINOR CONFORMER DISPLAYED A C2'-ENDO SUGAR PUCKER AND AN ANTI GLYCOSIDIC BOND. IT FORMED AN ANTI:ANTI BASE PAIR CONTAINING TWO HYDROGEN BONDS WITH THE OPPOSITE DG. THE MODIFIED DA RESIDUE OF THE MAJOR CONFORMER OF THIS MOLECULE [YEH ET AL. (1995) BIOCHEMISTRY 34, 13570-13581] DISPLAYED C3'-ENDO SUGAR PUCKER AND A SYN GLYCOSIDIC BOND. THE MAJOR CONFORMER MODIFIED DA RESIDUE FORMED A SYN:ANTI BASE PAIR CONTAINING NON-WATSON CRICK HYDROGEN BONDS WITH THE OPPOSITE DG. MORE REFINEMENT DETAILS CAN BE FOUND IN THE PRIMARY JOURNAL CITATION (SCHWARTZ ET AL.,1997).
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformers 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