[English] 日本語
Yorodumi
- PDB-8fdr: Structure of a dodecamer complex: 5'-CGCGAAAAGCCG-3-DB1476 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8fdr
TitleStructure of a dodecamer complex: 5'-CGCGAAAAGCCG-3-DB1476
Components
  • DNA (5'-D(*CP*GP*CP*GP*AP*AP*AP*AP*CP*GP*CP*G)-3')
  • DNA (5'-D(*CP*GP*CP*GP*TP*TP*TP*TP*CP*GP*CP*G)-3')
KeywordsDNA / AT sequence / Minor groove
Function / homologyChem-WFB / DNA / DNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsOgbonna, E. / Wilson, W.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM111749 United States
Citation
Journal: Acs Bio Med Chem Au / Year: 2023
Title: X-ray Structure Characterization of the Selective Recognition of AT Base Pair Sequences.
Authors: Ogbonna, E.N. / Paul, A. / Farahat, A.A. / Terrell, J.R. / Mineva, E. / Ogbonna, V. / Boykin, D.W. / Wilson, W.D.
#1: Journal: To be published
Title: X-ray Structure Characterization of the Selective Recognition of AT Base Pair Sequences
Authors: Ogbonna, E.N. / Paul, A. / Faharat, A. / Terrell, J.R. / Ogbonna, V. / Boykin, D.W. / Wilson, W.D.
History
DepositionDec 4, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)7,7054
Polymers7,3272
Non-polymers3792
Water1,35175
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)25.761, 39.840, 66.469
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

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


Mass: 3681.420 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: DNA chain DNA (5'-D(*CP*GP*CP*GP*TP*TP*TP*TP*CP*GP*CP*G)-3')


Mass: 3645.364 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-WFB / 4,4'-(1H-benzimidazole-2,6-diyl)di(benzene-1-carboximidamide)


Mass: 354.408 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H18N6
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 2.33 Å3/Da / Density % sol: 47.16 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: MPD, SODIUM CACODYLATE TRIHYDRATE, SPERMINE TETRACHLORIDE, SODIUM CHLORIDE, MAGNESIUM HEXAHYDRATE

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 28, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→25.52 Å / Num. obs: 104344 / % possible obs: 99.5 % / Redundancy: 2 % / Biso Wilson estimate: 24.4 Å2 / CC1/2: 1 / Net I/σ(I): 22.3
Reflection shellResolution: 1.55→1.605 Å / Num. unique obs: 1011 / CC1/2: 0.992

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
autoPROCdata reduction
XDSdata scaling
autoPROCdata processing
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→25.52 Å / SU ML: 0.146 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.3651
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2469 1040 10.01 %
Rwork0.2204 9352 -
obs0.223 10392 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.2 Å2
Refinement stepCycle: LAST / Resolution: 1.55→25.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 486 28 75 589
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0099574
X-RAY DIFFRACTIONf_angle_d1.2888879
X-RAY DIFFRACTIONf_chiral_restr0.064794
X-RAY DIFFRACTIONf_plane_restr0.014729
X-RAY DIFFRACTIONf_dihedral_angle_d29.5523258
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.630.30691450.29641302X-RAY DIFFRACTION99.31
1.63-1.730.3211420.2661287X-RAY DIFFRACTION98.28
1.73-1.870.2781460.23511306X-RAY DIFFRACTION99.73
1.87-2.060.33821480.25751331X-RAY DIFFRACTION99.93
2.06-2.350.26371500.24271344X-RAY DIFFRACTION100
2.35-2.960.28821500.27951353X-RAY DIFFRACTION100
2.97-25.520.20541590.18191429X-RAY DIFFRACTION99.37
Refinement TLS params.Method: refined / Origin x: 15.0772186674 Å / Origin y: 20.7722415333 Å / Origin z: 8.82441717769 Å
111213212223313233
T0.261416033974 Å2-0.00754593088558 Å20.0163294935679 Å2-0.241625963382 Å2-0.0146250450473 Å2--0.235401832891 Å2
L0.235201430147 °2-0.00619187153248 °20.562275209002 °2-0.736106164326 °21.4044185993 °2--5.05635320511 °2
S0.142154059178 Å °-0.0496586510107 Å °0.021052517946 Å °-0.140738302042 Å °0.129266555911 Å °-0.175013555208 Å °-0.373535045752 Å °-0.0487089286636 Å °-0.296983395125 Å °
Refinement TLS groupSelection details: all

+
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