[English] 日本語
Yorodumi
- PDB-465d: STRUCTURE OF THE TOPOISOMERASE II POISON BOUND TO DNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 465d
TitleSTRUCTURE OF THE TOPOISOMERASE II POISON BOUND TO DNA
ComponentsDNA (5'-D(*CP*GP*TP*AP*CP*G)-3')
KeywordsDNA / TOPOISOMERASE II POISON / HEXANUCLEOTIDE / D(CGTACG)2 / 9-AMINO-DACA
Function / homologyChem-9AD / DNA
Function and homology information
MethodX-RAY DIFFRACTION / ISOMORPHOUS REPLACEMENT / Resolution: 1.6 Å
AuthorsAdams, A. / Guss, J.M. / Collyer, C.A. / Denny, W.A. / Wakelin, L.P.
CitationJournal: Biochemistry / Year: 1999
Title: Crystal structure of the topoisomerase II poison 9-amino-[N-(2-dimethylamino)ethyl]acridine-4-carboxamide bound to the DNA hexanucleotide d(CGTACG)2.
Authors: Adams, A. / Guss, J.M. / Collyer, C.A. / Denny, W.A. / Wakelin, L.P.
History
DepositionApr 14, 1999Deposition site: NDB / Processing site: NDB
Revision 1.0Aug 25, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)2,4263
Polymers1,8091
Non-polymers6172
Water52229
1
A: DNA (5'-D(*CP*GP*TP*AP*CP*G)-3')
hetero molecules

A: DNA (5'-D(*CP*GP*TP*AP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,8526
Polymers3,6182
Non-polymers1,2344
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_655-x+1,-y,z1
Unit cell
Length a, b, c (Å)30.161, 30.161, 39.692
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Cell settinghexagonal
Space group name H-MP64
Components on special symmetry positions
IDModelComponents
11A-4025-

HOH

21A-4029-

HOH

-
Components

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


Mass: 1809.217 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Chemical ChemComp-9AD / 9-AMINO-(N-(2-DIMETHYLAMINO)ETHYL)ACRIDINE-4-CARBOXAMIDE


Mass: 308.378 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H20N4O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.76 Å3/Da / Density % sol: 55.41 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.5 MM DNA, 20 MM SODIUM CACODYLATE BUFFER, PH 6.5, 4 MM MAGNESIUM ACETATE, 1 MM COBALT(II) CHLORIDE, 0.33 MM SPERMINE.4HCL, 1 MM 9-AMINO-[N-(2- DIMETHYLAMINO)ETHYL]ACRIDINE-4-CARBOXAMIDE ...Details: 0.5 MM DNA, 20 MM SODIUM CACODYLATE BUFFER, PH 6.5, 4 MM MAGNESIUM ACETATE, 1 MM COBALT(II) CHLORIDE, 0.33 MM SPERMINE.4HCL, 1 MM 9-AMINO-[N-(2- DIMETHYLAMINO)ETHYL]ACRIDINE-4-CARBOXAMIDE AND 9% MPD EQUILIBRATED AGAINST 1 ML OF A SOLUTION OF 45% MPD IN WATER, VAPOR DIFFUSION, SITTING DROP, temperature 285K
Components of the solutions
IDNameCrystal-IDSol-ID
1SODIUM CACODYLATE11
2MAGNESIUM ACETATE11
3COCL211
4SPERMINE11
5MPD11
6MPD12
Crystal grow
*PLUS
Temperature: 285 K
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.5 mMDNA1drop
220 mMsodium cacodylate1drop
34 mMmagnesium acetate1drop
41 mM1dropCoCl2
50.33 mMspermine-4HCl1drop
61 mM9-amino-DACA-2HCl1drop
79 %MPD1drop
845 %MPD1reservoir

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Dec 12, 1997 / Details: FOCUSING MIRROR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. all: 2763 / Num. obs: 2763 / % possible obs: 98.4 % / Observed criterion σ(I): 0 / Redundancy: 24.7 % / Rmerge(I) obs: 0.029 / Net I/σ(I): 56.8
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.142 / Mean I/σ(I) obs: 5 / % possible all: 97
Reflection
*PLUS
Num. measured all: 67055
Reflection shell
*PLUS
% possible obs: 97 %

-
Processing

Software
NameClassification
SHELXSphasing
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: ISOMORPHOUS REPLACEMENT
Starting model: DDF073

Resolution: 1.6→16 Å / Num. parameters: 791 / Num. restraintsaints: 999 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.256 225 8.3 %RANDOM
Rwork0.1934 ---
all0.1958 2705 --
obs0.1945 2705 98.5 %-
Solvent computationSolvent model: MOEWS & KRETSINGER,J.MOL.BIOL.91(1973)201-228
Refine analyzeNum. disordered residues: 1 / Occupancy sum non hydrogen: 182.5
Refinement stepCycle: LAST / Resolution: 1.6→16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 120 46 29 195
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.01
X-RAY DIFFRACTIONs_angle_d0.021
X-RAY DIFFRACTIONs_similar_dist0.038
X-RAY DIFFRACTIONs_from_restr_planes0.023
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.6 Å / σ(F): 0 / % reflection Rfree: 8.3 % / Rfactor obs: 0.193
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: s_plane_restr / Dev ideal: 0.023

+
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://pdbjlc1.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