[English] 日本語
Yorodumi
- PDB-1eg6: CRYSTAL STRUCTURE ANALYSIS OF D(CG(5-BRU)ACG) COMPLEXES TO A PHENAZINE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1eg6
TitleCRYSTAL STRUCTURE ANALYSIS OF D(CG(5-BRU)ACG) COMPLEXES TO A PHENAZINE
Components5'-D(*CP*GP*(BRO)UP*AP*CP*G)-3'
KeywordsDNA / DRUG-DNA COMPLEX / INTERCALATION / MAJOR GROOVE BINDING / DOUBLE HELIX
Function / homologyCOBALT (III) ION / Chem-BFA / BROMIDE ION / DNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsCardin, C.J. / Denny, W.A. / Hobbs, J.R. / Thorpe, J.H.
CitationJournal: Biochemistry / Year: 2000
Title: Guanine specific binding at a DNA junction formed by d[CG(5-BrU)ACG](2) with a topoisomerase poison in the presence of Co(2+) ions.
Authors: Thorpe, J.H. / Hobbs, J.R. / Todd, A.K. / Denny, W.A. / Charlton, P. / Cardin, C.J.
History
DepositionFeb 14, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 3, 2001Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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*(BRO)UP*AP*CP*G)-3'
B: 5'-D(*CP*GP*(BRO)UP*AP*CP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,2417
Polymers3,5902
Non-polymers6515
Water66737
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)29.420, 53.440, 41.320
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Cell settingorthorhombic
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11A-40-

3CO

21B-50-

BFA

31A-56-

HOH

-
Components

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


Mass: 1795.191 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Chemical ChemComp-3CO / COBALT (III) ION / Cobalt


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#3: Chemical ChemComp-BR / BROMIDE ION / Bromide


Mass: 79.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Br
#4: Chemical ChemComp-BFA / 9-BROMO-PHENAZINE-1-CARBOXYLIC ACID (2-DIMETHYLAMINO-ETHYL)-AMIDE


Mass: 373.247 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H17BrN4O
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 2.15 Å3/Da / Density % sol: 42.71 %
Crystal growTemperature: 279 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: DROP: SODIUM CACODYLATE BUFFER, MAGNESIUM ACETATE, COBALT CHLORIDE, SPERMINE, MPD RESERVOIR: MPD, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 279K
Components of the solutions
IDNameCrystal-IDSol-ID
1SODIUM CACODYLATE11
2MAGNESIUM ACETATE11
3CoCl311
4SPERMINE11
5MPD11
6MPD12
Crystal grow
*PLUS
Temperature: 291 K / pH: 6.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
10.05 mMDNA1dropdouble stranded conc.
20.1 mMdrug1drop
38 mMsodium cacodylate1drop
44 mM1dropMg(OAc)2
52.4 mM1dropCoCl2
66 %1drop
735 %MPD1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 0.9
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 6, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2→15 Å / Num. all: 2360 / Num. obs: 1566 / % possible obs: 78.8 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 2 / Redundancy: 4.79 % / Biso Wilson estimate: 29.312 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 8.35
Reflection shellHighest resolution: 2 Å / Redundancy: 1.29 % / Rmerge(I) obs: 0.026 / % possible all: 72.6

-
Processing

Software
NameVersionClassification
SOLVEphasing
SHELXL-97refinement
DENZOdata reduction
CCP4(SCALA)data scaling
RefinementResolution: 2→15 Å / Cross valid method: THROUGHOUT / σ(F): 4 / σ(I): 2 / Stereochemistry target values: 0
RfactorNum. reflection% reflectionSelection details
Rfree0.3469 104 6.6 %RANDOM
Rwork0.2276 ---
all0.2501 2091 --
obs0.2276 1566 78.81 %-
Refinement stepCycle: LAST / Resolution: 2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 222 50 37 309
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
σ(F): 4 / % reflection Rfree: 6.6 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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