[English] 日本語
Yorodumi
- PDB-366d: 1.3 A STRUCTURE DETERMINATION OF THE D(CG(5-BRU)ACG)2/6-BROMO-9-A... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 366d
Title1.3 A STRUCTURE DETERMINATION OF THE D(CG(5-BRU)ACG)2/6-BROMO-9-AMINO-DACA COMPLEX
ComponentsDNA (5'-D(*CP*GP*(BRU)P*AP*CP*G)-3')
KeywordsDNA / DRUG INTERCALATION / MAJOR GROOVE BINDING
Function / homologyChem-DA6 / DNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO / Resolution: 1.3 Å
AuthorsTodd, A.K. / Adams, A. / Thorpe, J.H. / Denny, W.A. / Cardin, C.J.
CitationJournal: J.Med.Chem. / Year: 1999
Title: Major groove binding and 'DNA-induced' fit in the intercalation of a derivative of the mixed topoisomerase I/II poison N-(2-(dimethylamino)ethyl)acridine-4-carboxamide (DACA) into DNA: X-ray ...Title: Major groove binding and 'DNA-induced' fit in the intercalation of a derivative of the mixed topoisomerase I/II poison N-(2-(dimethylamino)ethyl)acridine-4-carboxamide (DACA) into DNA: X-ray structure complexed to d(CG(5-BrU)ACG)2 at 1.3-A resolution.
Authors: Todd, A.K. / Adams, A. / Thorpe, J.H. / Denny, W.A. / Wakelin, L.P. / Cardin, C.J.
History
DepositionDec 19, 1997Deposition site: NDB / Processing site: NDB
Revision 1.0Apr 6, 1999Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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: DNA (5'-D(*CP*GP*(BRU)P*AP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,6533
Polymers1,8741
Non-polymers7792
Water54030
1
A: DNA (5'-D(*CP*GP*(BRU)P*AP*CP*G)-3')
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)5,3056
Polymers3,7482
Non-polymers1,5574
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_655-x+1,-y,z1
Unit cell
Length a, b, c (Å)30.110, 30.110, 39.560
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-3015-

DA6

21A-3015-

DA6

31A-3015-

DA6

41A-3015-

DA6

-
Components

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


Mass: 1874.087 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: COMPLEXED WITH 6-BROMO-9-AMINO-N-ETHYL(DIAMINOMETHYL)ACRIDINE-4-CARBOXAMIDE
#2: Chemical ChemComp-DA6 / 6-BROMO-9-AMINO-N-ETHYL(DIAMINOMETHYL)ACRIDINE-4-CARBOXAMIDE / 6BR20686


Mass: 389.290 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H21BrN4O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 2.74 Å3/Da / Density % sol: 54 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.5 / Details: pH 6.5, VAPOR DIFFUSION, HANGING DROP
Components of the solutions
IDNameCrystal-IDSol-ID
1SODIUM CACODYLATE11
2MGCL211
3SPERMINE11
4MPD11
Crystal grow
*PLUS
Temperature: 285 K / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.5 mMDNA1drop
250 mMcacodylate1drop
32.0 mMmagnesium acetate1drop
43.0 mMsperine-4HCl1drop
55 %MPD1drop
630 %MPD1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 14, 1997 / Details: MIRRORS
RadiationMonochromator: SI 111 CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→8 Å / Num. obs: 9362 / % possible obs: 95.3 % / Redundancy: 3.91 % / Rmerge(I) obs: 0.06
Reflection
*PLUS
Num. obs: 9306 / Num. measured all: 31514 / Rmerge(I) obs: 0.0675
Reflection shell
*PLUS
Highest resolution: 1.3 Å / Lowest resolution: 1.4 Å / % possible obs: 37 %

-
Processing

Software
NameClassification
SHELXSphasing
SHELXL-96refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: AB INITIO / Resolution: 1.3→8 Å / Num. parameters: 3275 / Num. restraintsaints: 8013
RfactorNum. reflection% reflection
all0.185 8867 -
obs--90.2 %
Refine analyzeNum. disordered residues: 1 / Occupancy sum non hydrogen: 401.5
Refinement stepCycle: LAST / Resolution: 1.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 215 91 30 336
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.002
X-RAY DIFFRACTIONs_angle_d0.02
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes
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-96 / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.1468
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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