[English] 日本語
Yorodumi
- PDB-5xk0: Structure of 8-mer DNA2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5xk0
TitleStructure of 8-mer DNA2
ComponentsDNA (5'-D(*GP*CP*CP*CP*GP*AP*GP*C)-3')
KeywordsDNA / duplex
Function / homologyDNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.451 Å
AuthorsLiu, H.H. / Gan, J.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31370728 China
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2017
Title: A DNA Structure Containing AgI -Mediated G:G and C:C Base Pairs
Authors: Liu, H.H. / Shen, F.S. / Haruehanroengra, P. / Yao, Q.Q. / Cheng, Y.S. / Chen, Y.Q. / Yang, C. / Zhang, J. / Wu, B.X. / Luo, Q. / Cui, R.X. / Li, J.X. / Ma, J.B. / Sheng, J. / Gan, J.H.
History
DepositionMay 4, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA (5'-D(*GP*CP*CP*CP*GP*AP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)2,4131
Polymers2,4131
Non-polymers00
Water64936
1
A: DNA (5'-D(*GP*CP*CP*CP*GP*AP*GP*C)-3')

A: DNA (5'-D(*GP*CP*CP*CP*GP*AP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)4,8252
Polymers4,8252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area760 Å2
ΔGint-5 kcal/mol
Surface area3080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.012, 42.012, 25.016
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

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


Mass: 2412.594 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 2.29 Å3/Da / Density % sol: 46.23 % / Description: diamond
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 10% v/v MPD, 40mM Sodium cacodylate pH 6.0, 12mM Spermine tetra-HCl, 80mM KCl, 20mM MgCl2

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.45→30 Å / Num. obs: 4199 / % possible obs: 98.6 % / Redundancy: 19.8 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 82.3
Reflection shellResolution: 1.45→1.5 Å / Redundancy: 13.8 % / Rmerge(I) obs: 0.358 / Mean I/σ(I) obs: 12.9 / Num. unique obs: 358 / % possible all: 87.5

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5WSP

5wsp


Resolution: 1.451→29.707 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.42 / Phase error: 18.6
RfactorNum. reflection% reflection
Rfree0.1956 190 4.52 %
Rwork0.1803 --
obs0.181 4199 98.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.451→29.707 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 160 0 36 196
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006179
X-RAY DIFFRACTIONf_angle_d0.919274
X-RAY DIFFRACTIONf_dihedral_angle_d14.5676
X-RAY DIFFRACTIONf_chiral_restr0.04131
X-RAY DIFFRACTIONf_plane_restr0.0098
LS refinement shellResolution: 1.4513→1.5 Å
RfactorNum. reflection% reflection
Rfree0.1956 190 -
Rwork0.1823 345 -
obs--98 %
Refinement TLS params.Method: refined / Origin x: 9.5067 Å / Origin y: 9.0897 Å / Origin z: 2.4899 Å
111213212223313233
T0.223 Å20.001 Å20.0392 Å2-0.1966 Å20.0085 Å2--0.1895 Å2
L1.7947 °2-1.927 °2-0.0487 °2-6.1765 °22.0046 °2--2.133 °2
S-0.1305 Å °-0.1571 Å °0.0532 Å °0.6226 Å °0.195 Å °-0.0137 Å °0.0978 Å °-0.0281 Å °-0.059 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