[English] 日本語
Yorodumi
- PDB-8bag: Copper(II) bound to a non-canonical quadruplex containing the dam... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8bag
TitleCopper(II) bound to a non-canonical quadruplex containing the damaged base 8-oxoguanine
ComponentsDNA (5'-D(*(8OG)P*CP*AP*TP*GP*CP*T)-3')
KeywordsDNA
Function / homologyCOPPER (II) ION / COBALT HEXAMMINE(III) / DNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.13 Å
AuthorsLambert, M.C. / Hall, J.P.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Engineering and Physical Sciences Research Council United Kingdom
CitationJournal: To Be Published
Title: Oxidative damage induce copper(II)-DNA binding
Authors: Lambert, M.C. / Brazier, J.A. / Cardin, C.J. / Hall, J.P.
History
DepositionOct 11, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 25, 2023Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA (5'-D(*(8OG)P*CP*AP*TP*GP*CP*T)-3')
B: DNA (5'-D(*(8OG)P*CP*AP*TP*GP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,0308
Polymers4,2592
Non-polymers7726
Water91951
1
A: DNA (5'-D(*(8OG)P*CP*AP*TP*GP*CP*T)-3')
hetero molecules

A: DNA (5'-D(*(8OG)P*CP*AP*TP*GP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,67512
Polymers4,2592
Non-polymers1,41610
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
2
B: DNA (5'-D(*(8OG)P*CP*AP*TP*GP*CP*T)-3')
hetero molecules

B: DNA (5'-D(*(8OG)P*CP*AP*TP*GP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,3864
Polymers4,2592
Non-polymers1272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Unit cell
Length a, b, c (Å)21.990, 58.870, 45.460
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-102-

NCO

21B-219-

HOH

31B-225-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and resid 2 through 5)
d_2ens_1(chain "B" and resid 2 through 5)

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-ID
d_11ens_1DCDGA
d_21ens_1DCDGB

NCS oper: (Code: givenMatrix: (0.99886184781, -0.0401425817238, 0.0257600877856), (-0.0399546431106, -0.999171286283, -0.00776963073116), (0.0260506330841, 0.00673155259496, -0.999637959821)Vector: 0. ...NCS oper: (Code: given
Matrix: (0.99886184781, -0.0401425817238, 0.0257600877856), (-0.0399546431106, -0.999171286283, -0.00776963073116), (0.0260506330841, 0.00673155259496, -0.999637959821)
Vector: 0.169549702879, 8.69758057536, 22.6863258865)

-
Components

#1: DNA chain DNA (5'-D(*(8OG)P*CP*AP*TP*GP*CP*T)-3')


Mass: 2129.410 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CoH18N6
#3: Chemical ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.73 Å3/Da / Density % sol: 28.79 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.7
Details: 2 ul 40 mM sodium cacodylate, 1 ul 80 mM hexammine (III) cobalt, 1 ul 10% MPD, 2 ul 800 mM potassium chloride, ul 30 mM sodium chloride, 2 ul 1 mM DNA

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97624 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Nov 25, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97624 Å / Relative weight: 1
ReflectionResolution: 1.13→29.43 Å / Num. obs: 11191 / % possible obs: 97.89 % / Redundancy: 1 % / Biso Wilson estimate: 11.75 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.07 / Net I/σ(I): 15.3
Reflection shellResolution: 1.13→1.15 Å / Rmerge(I) obs: 0.964 / Num. unique obs: 495 / CC1/2: 0.756

-
Processing

Software
NameVersionClassification
xia2data scaling
XDSdata reduction
PHASERphasing
Cootmodel building
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MF5

1mf5


Resolution: 1.13→29.43 Å / SU ML: 0.0994 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.7633
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1724 995 4.77 %
Rwork0.1518 19865 -
obs0.1528 11162 97.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.66 Å2
Refinement stepCycle: LAST / Resolution: 1.13→29.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 282 30 51 363
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0166344
X-RAY DIFFRACTIONf_angle_d1.7557557
X-RAY DIFFRACTIONf_chiral_restr0.078654
X-RAY DIFFRACTIONf_plane_restr0.011714
X-RAY DIFFRACTIONf_dihedral_angle_d31.0925120
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.488060752785 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.13-1.190.26621150.24222647X-RAY DIFFRACTION91.46
1.19-1.260.20181090.18232874X-RAY DIFFRACTION96.91
1.26-1.360.19321650.16242836X-RAY DIFFRACTION98.3
1.36-1.50.18481580.15882847X-RAY DIFFRACTION98.62
1.5-1.720.17791470.14982871X-RAY DIFFRACTION99.08
1.72-2.160.18811480.14932890X-RAY DIFFRACTION99.7
2.16-29.430.15261530.14022900X-RAY DIFFRACTION99.64

+
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