[English] 日本語
Yorodumi
- PDB-1dn4: SOLVATION OF THE LEFT-HANDED HEXAMER D(5BRC-G-5BRC-G-5BRC-G) IN C... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1dn4
TitleSOLVATION OF THE LEFT-HANDED HEXAMER D(5BRC-G-5BRC-G-5BRC-G) IN CRYSTALS GROWN AT TWO TEMPERATURES
ComponentsDNA (5'-D(*(CBR)P*GP*(CBR)P*GP*(CBR)P*G)-3')
KeywordsDNA / Z-DNA / DOUBLE HELIX / MODIFIED
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 1.6 Å
AuthorsChevrier, B. / Dock, A.C. / Hartmann, B. / Leng, M. / Moras, D. / Thuong, M.T. / Westhof, E.
CitationJournal: J.Mol.Biol. / Year: 1986
Title: Solvation of the left-handed hexamer d(5BrC-G-5BrC-G-5 BrC-G) in crystals grown at two temperatures.
Authors: Chevrier, B. / Dock, A.C. / Hartmann, B. / Leng, M. / Moras, D. / Thuong, M.T. / Westhof, E.
History
DepositionDec 1, 1986Deposition site: BNL / Processing site: BNL
Revision 1.0Apr 16, 1987Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
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_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA (5'-D(*(CBR)P*GP*(CBR)P*GP*(CBR)P*G)-3')
B: DNA (5'-D(*(CBR)P*GP*(CBR)P*GP*(CBR)P*G)-3')


Theoretical massNumber of molelcules
Total (without water)4,0942
Polymers4,0942
Non-polymers00
Water1,09961
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)18.010, 30.880, 44.760
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note2: ATOM HOH 1 IS PROBABLY A SODIUM ION.

-
Components

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


Mass: 2046.893 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

Crystal growTemperature: 291 K / Method: vapor diffusion / Details: VAPOR DIFFUSION, temperature 291.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3NACL11
4NA CACODYLATE11
5WATER12
6MPD12
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 6.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mMsodium cacodylate1drop
2200 mM1dropNaCl
31 mg/mlprotein1drop
410-60 %MPD1reservoir
51
61

-
Data collection

DiffractionMean temperature: 291 K
DetectorType: ENRAF-NONIUS CAD4 / Detector: DIFFRACTOMETER
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.6→10 Å / Num. all: 3195 / Num. obs: 2919 / Observed criterion σ(F): 3
Reflection
*PLUS
Highest resolution: 1.4 Å / Lowest resolution: 10 Å / Observed criterion σ(F): 2

-
Processing

SoftwareName: NUCLSQ / Classification: refinement
RefinementResolution: 1.6→10 Å / Occupancy max: 1 / Occupancy min: 0.44 / σ(F): 3 /
RfactorNum. reflection
obs0.1327 3195
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL SOLVENTSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 1.6→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 240 6 61 307
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.4 Å / Lowest resolution: 10 Å / σ(F): 3
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONp_bond_d
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr

+
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://pdbjlvh1.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