[English] 日本語
Yorodumi
- PDB-1g5l: CO(III)-BLEOMYCIN-OOH BOUND TO AN OLIGONUCLEOTIDE CONTAINING A PH... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1g5l
TitleCO(III)-BLEOMYCIN-OOH BOUND TO AN OLIGONUCLEOTIDE CONTAINING A PHOSPHOGLYCOLATE LESION
Components
  • 5'-D(*CP*CP*AP*AP*AP*G)-3'
  • 5'-D(*CP*CP*CP*AP*GP*TP*AP*CP*TP*TP*TP*GP*G)-3'
  • 5'-D(P*AP*CP*TP*GP*GP*G)-3'
KeywordsDNA / damaged DNA / DNA-drug complex / intercalation
Function / homologyCOBALT (III) ION / BLEOMYCIN B2 / OXYGEN ATOM / HYDROGEN PEROXIDE / 2-PHOSPHOGLYCOLIC ACID / DNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / molecular dynamics
AuthorsHoehn, S.T. / Junker, H.-D. / Bunt, R.C. / Turner, C.J. / Stubbe, J.
CitationJournal: Biochemistry / Year: 2001
Title: Solution structure of Co(III)-bleomycin-OOH bound to a phosphoglycolate lesion containing oligonucleotide: implications for bleomycin-induced double-strand DNA cleavage.
Authors: Hoehn, S.T. / Junker, H.D. / Bunt, R.C. / Turner, C.J. / Stubbe, J.
History
DepositionNov 1, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2001Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)9,2868
Polymers7,5943
Non-polymers1,6915
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 10all calculated structures submitted
Representative

-
Components

-
DNA chain , 3 types, 3 molecules ABC

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


Mass: 1802.232 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(P*AP*CP*TP*GP*GP*G)-3'


Mass: 1849.241 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain 5'-D(*CP*CP*CP*AP*GP*TP*AP*CP*TP*TP*TP*GP*G)-3'


Mass: 3942.572 Da / Num. of mol.: 1 / Source method: obtained synthetically

-
Non-polymers , 5 types, 5 molecules

#4: Chemical ChemComp-PGA / 2-PHOSPHOGLYCOLIC ACID


Mass: 156.031 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C2H5O6P
#5: Chemical ChemComp-3CO / COBALT (III) ION / Cobalt


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#6: Chemical ChemComp-O / OXYGEN ATOM / Oxygen


Mass: 15.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O
#7: Chemical ChemComp-BLB / BLEOMYCIN B2


Mass: 1426.515 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C55H85N20O21S2
#8: Chemical ChemComp-PEO / HYDROGEN PEROXIDE / Hydrogen peroxide


Mass: 34.015 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O2

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121TOCSY
131PE-COSY
242WATERGATE-NOESY
15131P-HCOSY
16113C-HSQC
171ROESY
NMR detailsText: DNA was synthesized as a double hairpin, but for modeling purposed was treated as two strands of DNA; the hexaethylene glycol spacers were not included in the modeling

-
Sample preparation

Details
Solution-IDContentsSolvent system
11.25 mM drug-DNA complex; 40 mM sodium phosphate bufferD2O
21.25 mM drug-DNA complex; 40 mM sodium phosphate buffer90% H2O/10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
140 mM sodium phosphate buffer 6.8 ambient 293 K
240 mM sodium phosphate buffer 6.8 ambient 278 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Home-built home builtHome-builthome built7501
Home-built home builtHome-builthome built6002

-
Processing

NMR software
NameVersionDeveloperClassification
Felix95MSIprocessing
X-PLOR3.851Brungerstructure solution
Felix95MSIdata analysis
X-PLOR3.851Brungerrefinement
RefinementMethod: molecular dynamics / Software ordinal: 1
Details: The structures are based on 729 NOE-derived distance constraints and 96 dihedral angle restraints.
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 10 / Conformers submitted total number: 10

+
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