[English] 日本語
Yorodumi
- PDB-427d: 5'-D(*CP*GP*CP*(CH2-DM1)GP*CP*G)-3' -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 427d
Title5'-D(*CP*GP*CP*(CH2-DM1)GP*CP*G)-3'
ComponentsDNA (5'-D(*CP*GP*CP*(G49)P*CP*G)-3')
KeywordsDNA / DEOXYRIBONUCLEIC ACID / DRUG COMPLEX / FORMALDEHYDE CROSS-LINK / ATOMIC RESOLUTION / DOUBLE BACKBONE CONFORMATION
Function / homologyDAUNOMYCIN / DNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.1 Å
AuthorsSchuerman, G. / Van Meervelt, L.
CitationJournal: J.Am.Chem.Soc. / Year: 2000
Title: Conformational Flexibility of the DNA Backbone.
Authors: Schuerman, G. / Van Meervelt, L.
History
DepositionSep 21, 1998Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 24, 2000Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
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_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_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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*CP*(G49)P*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,3522
Polymers1,8241
Non-polymers5281
Water1,17165
1
A: DNA (5'-D(*CP*GP*CP*(G49)P*CP*G)-3')
hetero molecules

A: DNA (5'-D(*CP*GP*CP*(G49)P*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,7044
Polymers3,6482
Non-polymers1,0552
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Unit cell
Length a, b, c (Å)27.818, 27.818, 51.858
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Cell settingtetragonal
Space group name H-MP41212

-
Components

#1: DNA chain DNA (5'-D(*CP*GP*CP*(G49)P*CP*G)-3')


Mass: 1824.232 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Chemical ChemComp-DM1 / DAUNOMYCIN / DAUNORUBICIN / Daunorubicin


Mass: 527.520 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H29NO10 / Comment: medication, chemotherapy*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 2.63 Å3/Da / Density % sol: 53.31 % / Description: DDF023 USED AS STARTING MODEL FOR REFINEMENT
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Components of the solutions
IDNameCrystal-IDSol-ID
1SODIUM CACODYLATE11
2NACLSodium chloride11
3BACL211
4SPERMINE11
5MPD11
6MPD12
Crystal grow
*PLUS
Temperature: 16 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
14.0 mMoligonucleotide1drop
26.4 mMdaunomycin HCl1drop
310 %MPD1drop
412 mMspermine tetrachloride1drop
580 mM1dropNaCl
620 mM1dropBaCl2
835 %MPD1reservoir
7sodium cacodylate1drop

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 15, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.1→15 Å / Num. all: 8581 / Num. obs: 8581 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Rmerge(I) obs: 0.041 / Net I/σ(I): 25.27
Reflection shellResolution: 1.1→1.12 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.094 / Mean I/σ(I) obs: 10.58 / % possible all: 77
Reflection
*PLUS
% possible obs: 97.3 %
Reflection shell
*PLUS
% possible obs: 77 % / Num. unique obs: 338

-
Processing

Software
NameClassification
SHELXLrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementStarting model: DDF023

Resolution: 1.1→15 Å / Num. parameters: 2327 / σ(F): 4 / Details: ANISOTROPIC UNRESTRAINED REFIN.
RfactorNum. reflection% reflection
all0.1021 8581 -
obs0.1007 -97.5 %
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201- 228
Refine analyzeNum. disordered residues: 27 / Occupancy sum hydrogen: 222.47 / Occupancy sum non hydrogen: 97
Refinement stepCycle: LAST / Resolution: 1.1→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 182 0 75 257
Software
*PLUS
Name: SHELXL-96 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 8277 / Rfactor all: 0.102 / Rfactor obs: 0.101
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