[English] 日本語
Yorodumi
- PDB-1s1l: Influence of Groove Interactions on the Formation of DNA Holliday... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1s1l
TitleInfluence of Groove Interactions on the Formation of DNA Holliday Junctions
Components5'-D(*CP*CP*(OIP)*GP*TP*AP*CP*(5CM)P*GP*G)-3'
KeywordsDNA / Holliday Junction / DNA Four-Way Junction / major groove / Inosine / minor groove
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsHays, F.A. / Jones, Z.J. / Ho, P.S.
CitationJournal: Biochemistry / Year: 2004
Title: Influence of minor groove substituents on the structure of DNA holliday junctions.
Authors: Hays, F.A. / Jones, Z.J. / Ho, P.S.
History
DepositionJan 6, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Feb 14, 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
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). THE FULL BIOLOGICAL UNIT CONSISTS OF A FOUR STRANDED DNA HOLLIDAY JUNCTION. SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S).

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 5'-D(*CP*CP*(OIP)*GP*TP*AP*CP*(5CM)P*GP*G)-3'
B: 5'-D(*CP*CP*(OIP)*GP*TP*AP*CP*(5CM)P*GP*G)-3'


Theoretical massNumber of molelcules
Total (without water)6,0902
Polymers6,0902
Non-polymers00
Water1,11762
1
A: 5'-D(*CP*CP*(OIP)*GP*TP*AP*CP*(5CM)P*GP*G)-3'
B: 5'-D(*CP*CP*(OIP)*GP*TP*AP*CP*(5CM)P*GP*G)-3'

A: 5'-D(*CP*CP*(OIP)*GP*TP*AP*CP*(5CM)P*GP*G)-3'
B: 5'-D(*CP*CP*(OIP)*GP*TP*AP*CP*(5CM)P*GP*G)-3'


Theoretical massNumber of molelcules
Total (without water)12,1804
Polymers12,1804
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Unit cell
Length a, b, c (Å)64.923, 24.869, 37.095
Angle α, β, γ (deg.)90.00, 109.22, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-49-

HOH

DetailsFull four stranded Holliday junction structure is generated by a 2-fold symmetry axis.

-
Components

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


Mass: 3045.006 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 2.17 Å3/Da / Density % sol: 42.8 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 7
Details: 25mM Na Cacodylate, .5mM DNA, 180mM CaCl2, 2.4mM spermine against 20% resevoir MPD, pH 7.0, VAPOR DIFFUSION, SITTING DROP
Components of the solutions
IDNameCrystal-IDSol-ID
1Na Cacodylate11
2.5mM DNA11
3CaCl211
4spermine11
5MPD12
6Na Cacodylate12

-
Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.542 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 8, 2003 / Details: osmic mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 2→18.2 Å / Num. all: 3492 / Num. obs: 3492 / % possible obs: 93.4 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 11.2 Å2 / Rmerge(I) obs: 0.05
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.291 / Mean I/σ(I) obs: 2.4 / % possible all: 61.8

-
Processing

Software
NameVersionClassification
CNS1.1refinement
SCALEPACKdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ndb id UD0019

Resolution: 2.2→18.2 Å / Rfactor Rfree error: 0.015 / Data cutoff high absF: 44978.75 / Data cutoff high rms absF: 44978.75 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.258 286 10 %RANDOM
Rwork0.236 ---
all0.266 3492 --
obs0.236 2852 96.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.3728 Å2 / ksol: 0.360393 e/Å3
Displacement parametersBiso mean: 11.2 Å2
Baniso -1Baniso -2Baniso -3
1-2.08 Å20 Å2-1.93 Å2
2--2.33 Å20 Å2
3----4.41 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.37 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 2.2→18.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 404 0 62 466
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.003
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg0.8
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d18.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.28
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.053 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.334 40 9.3 %
Rwork0.267 391 -
obs--88 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP

+
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