[English] 日本語
Yorodumi
- PDB-2o1i: RH(BPY)2CHRYSI complexed to mismatched DNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2o1i
TitleRH(BPY)2CHRYSI complexed to mismatched DNA
Components5'-D(*CP*GP*GP*AP*AP*AP*TP*TP*CP*CP*CP*G)-3'
KeywordsDNA / DNA mismatch / metallointercalator / DNA recognition
Function / homologyChem-R1C / DNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO / Resolution: 1.1 Å
AuthorsPierre, V.C. / Kaiser, J.T. / Barton, J.K.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Insights into finding a mismatch through the structure of a mispaired DNA bound by a rhodium intercalator.
Authors: Pierre, V.C. / Kaiser, J.T. / Barton, J.K.
History
DepositionNov 28, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 9, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_special_symmetry / 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(*CP*GP*GP*AP*AP*AP*TP*TP*CP*CP*CP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,6564
Polymers3,6471
Non-polymers2,0093
Water1,35175
1
A: 5'-D(*CP*GP*GP*AP*AP*AP*TP*TP*CP*CP*CP*G)-3'
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)11,3128
Polymers7,2952
Non-polymers4,0176
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Unit cell
Length a, b, c (Å)38.740, 38.740, 57.560
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-1001-

R1C

21A-2013-

HOH

DetailsThe second part of the biological assembly is generated by the two fold axis y,x,-z.

-
Components

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


Mass: 3647.393 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: solid phase synthesis
#2: Chemical ChemComp-R1C / bis(2,2'-bipyridine-kappa~2~N~1~,N~1'~)[chrysene-5,6-diiminato(2-)-kappa~2~N,N']rhodium(4+) / DELTA-Rhodium(III)- bis-(2,2'-bipyridyl)-5,6-chrysenequinone diimine


Mass: 669.559 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C38H26N6Rh
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / 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 Å3/Da / Density % sol: 56.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: SrCl2 40mM, MgCl2 10mM, Na-cacodylate 20mM, spermine-4HCl 6mM, MPD 5%(v/v)equilibrated against 35% MPD, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1SrCl211
2MgCl211
3Na-cacodylate11
4spermine-4HCl11
5MPD11
6HOH11
7SrCl212
8MgCl212
9Na-cacodylate12
10MPD12
11HOH12

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
ROTATING ANODERIGAKU11.5418
SYNCHROTRONSSRL BL11-121.03317
Detector
TypeIDDetectorDate
RIGAKU RAXIS IV1IMAGE PLATEMay 5, 2006
ADSC QUANTUM 3152CCDMay 19, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
21.033171
ReflectionResolution: 1.1→24 Å / Num. obs: 17269 / % possible obs: 94 % / Redundancy: 8.7 % / Biso Wilson estimate: 14.85 Å2 / Rmerge(I) obs: 0.107 / Rsym value: 0.107 / Net I/σ(I): 13.4
Reflection shellResolution: 1.07→1.14 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.015 / Mean I/σ(I) obs: 0.9 / Rsym value: 1.5 / % possible all: 100

-
Processing

Software
NameVersionClassification
SHELXmodel building
SHELXL-97refinement
Blu-Icedata collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
SHELXDphasing
RefinementMethod to determine structure: AB INITIO / Highest resolution: 1.1 Å / Num. parameters: 4070 / Num. restraintsaints: 5578 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.204 --RANDOM
all0.1515 ---
obs-17269 94 %-
Refine analyzeNum. disordered residues: 2 / Occupancy sum hydrogen: 178 / Occupancy sum non hydrogen: 384
Refinement stepCycle: LAST / Highest resolution: 1.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 242 135 75 452
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.024
X-RAY DIFFRACTIONs_angle_d0.041
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0135
X-RAY DIFFRACTIONs_zero_chiral_vol0
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.022
X-RAY DIFFRACTIONs_anti_bump_dis_restr0
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.036
X-RAY DIFFRACTIONs_approx_iso_adps0.109

+
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