[English] 日本語
Yorodumi
- PDB-4gqj: Complex of a binuclear Ruthenium compound D,D-([mu-(11,11')-bi(dp... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4gqj
TitleComplex of a binuclear Ruthenium compound D,D-([mu-(11,11')-bi(dppz)-(1,10-phenanthroline)4-Ru2]4+) bound to d(CGTACG)
ComponentsDNA (5'-D(*CP*GP*TP*AP*CP*G)-3')
KeywordsDNA / DNA recognition / DNA binsinf
Function / homologyChem-RR2 / DNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.951 Å
AuthorsBoer, D.R. / Coll, M.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2014
Title: Thread Insertion of a Bis(dipyridophenazine) Diruthenium Complex into the DNA Double Helix by the Extrusion of AT Base Pairs and Cross-Linking of DNA Duplexes.
Authors: Boer, D.R. / Wu, L. / Lincoln, P. / Coll, M.
History
DepositionAug 23, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 5, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 28, 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
Revision 1.2Mar 13, 2024Group: Source and taxonomy / Structure summary / Category: entity / pdbx_entity_src_syn / Item: _entity.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA (5'-D(*CP*GP*TP*AP*CP*G)-3')
B: DNA (5'-D(*CP*GP*TP*AP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,1043
Polymers3,6182
Non-polymers1,4861
Water28816
1
A: DNA (5'-D(*CP*GP*TP*AP*CP*G)-3')
B: DNA (5'-D(*CP*GP*TP*AP*CP*G)-3')
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)10,2086
Polymers7,2374
Non-polymers2,9712
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation13_545y+3/4,x-3/4,-z+1/41
Unit cell
Length a, b, c (Å)85.429, 85.429, 85.429
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number213
Space group name H-MP4132

-
Components

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


Mass: 1809.217 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Acquired from biomers (Germany)
#2: Chemical ChemComp-RR2 / (mu-11,11'-bidipyrido[3,2-a:2',3'-c]phenazine-1kappa~2~N~4~,N~5~:2kappa~2~N~4'~,N~5'~)[tetrakis(1,10-phenanthroline-kappa~2~N~1~,N~10~)]diruthenium


Mass: 1485.543 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C84H50N16Ru2 / Details: Synthesized by citation authors
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O / Details: Synthesized by citation authors

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 7.18 Å3/Da / Density % sol: 82.87 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: buffer: 0.2 M KCl 10 mM MgCl2 35% hexanediol 50 mM TRIS.HCl pH 8 drop composition: 0.5 ul 10 mM binuclear Ru compound 0.5 ul 10 mM [ssDNA] 5'-d(CGTACG)-3' 1 ul cryst. buffer 0.5 ul , VAPOR ...Details: buffer: 0.2 M KCl 10 mM MgCl2 35% hexanediol 50 mM TRIS.HCl pH 8 drop composition: 0.5 ul 10 mM binuclear Ru compound 0.5 ul 10 mM [ssDNA] 5'-d(CGTACG)-3' 1 ul cryst. buffer 0.5 ul , VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.07205 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 14, 2009
RadiationMonochromator: channel-cut Si(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07205 Å / Relative weight: 1
ReflectionResolution: 2.95→50 Å / Num. all: 2419 / Num. obs: 2419 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Biso Wilson estimate: 73.4 Å2 / Rmerge(I) obs: 0.118 / Net I/σ(I): 10.3
Reflection shellResolution: 2.95→3.11 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 2.1 / Num. unique all: 343 / % possible all: 99

-
Processing

Software
NameVersionClassification
MxCuBEdata collection
SHELXSphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.951→38.205 Å / SU ML: 0.29 / σ(F): 1.36 / Phase error: 19.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2065 104 4.34 %RANDOM
Rwork0.1773 ---
obs0.1786 2396 95.34 %-
all-2419 --
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 19.848 Å2 / ksol: 0.272 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2--0 Å20 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 2.951→38.205 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 223 102 16 341
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007383
X-RAY DIFFRACTIONf_angle_d1.39579
X-RAY DIFFRACTIONf_dihedral_angle_d34.982123
X-RAY DIFFRACTIONf_chiral_restr0.08551
X-RAY DIFFRACTIONf_plane_restr0.00717
LS refinement shellHighest resolution: 2.9511 Å
RfactorNum. reflection% reflection
Rfree0.2065 104 -
Rwork0.1773 2292 -
obs--95 %

+
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