[English] 日本語
Yorodumi
- PDB-1jux: 1.6A Resolution Crystal Structures of the DNA Octamers d(IUATATAC... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1jux
Title1.6A Resolution Crystal Structures of the DNA Octamers d(IUATATAC) and d(ITITACAC):Binding of Two Distamycin Drugs Side-by-Side
Components5'-D(*IP*TP*IP*TP*AP*CP*AP*C)-3'
KeywordsDNA / Octamer / Distamycin / Side-by-Side
Function / homologyDISTAMYCIN A / DNA
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsDeng, J. / Pan, B. / Sundaralingam, M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Structure of d(ITITACAC) complexed with distamycin at 1.6 A resolution.
Authors: Deng, J. / Pan, B. / Sundaralingam, M.
History
DepositionAug 28, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Feb 7, 2024Group: 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 5'-D(*IP*TP*IP*TP*AP*CP*AP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,8782
Polymers2,3971
Non-polymers4821
Water64936
1
A: 5'-D(*IP*TP*IP*TP*AP*CP*AP*C)-3'
hetero molecules

A: 5'-D(*IP*TP*IP*TP*AP*CP*AP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,7564
Polymers4,7932
Non-polymers9632
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Unit cell
Length a, b, c (Å)33.260, 25.050, 28.300
Angle α, β, γ (deg.)90.00, 124.23, 90.00
Int Tables number5
Space group name H-MC121
DetailsOne strand in the assymetric unit. The duplex is generated by the 2 fold axis.

-
Components

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


Mass: 2396.589 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Octamer DNA
#2: Chemical ChemComp-DMY / DISTAMYCIN A / DISTAMYCIN / STALLIMYCIN


Mass: 481.508 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H27N9O4 / Comment: antibiotic*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 1.96 Å3/Da / Density % sol: 37.09 %
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
11 mMDNA1dropsingle-stranded concentration
230 mMsodium cacodylate1droppH7.0
30.1 mMcobalt hexammine chloride1drop
41 mMdistamycin hydrochloride1drop
560 %MPD1reservoir

-
Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jun 20, 1997
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→10 Å / Num. all: 2609 / Num. obs: 2468 / Observed criterion σ(F): 2
Reflection
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 10 Å / Num. obs: 2737 / % possible obs: 92 % / Rmerge(I) obs: 0.046
Reflection shell
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 1.7 Å / % possible obs: 88.8 % / Num. unique obs: 381 / Rmerge(I) obs: 0.162

-
Processing

Software
NameClassification
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→10 Å / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.179 234 -random
Rwork0.149 ---
all-2609 --
obs-2468 94.6 %-
Refinement stepCycle: LAST / Resolution: 1.6→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 159 35 36 230
Refinement
*PLUS
Lowest resolution: 10 Å / Num. reflection obs: 2520 / Rfactor Rfree: 0.207 / Rfactor Rwork: 0.17
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.006
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg1.3

+
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