[English] 日本語
Yorodumi
- PDB-5xk1: Structure of 8-mer DNA3 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5xk1
TitleStructure of 8-mer DNA3
ComponentsDNA (5'-D(*GP*GP*AP*GP*CP*CP*CP*C)-3')
KeywordsDNA / duplex
Function / homologyDNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.501 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*GP*AP*GP*CP*CP*CP*C)-3')
C: DNA (5'-D(*GP*GP*AP*GP*CP*CP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)4,8252
Polymers4,8252
Non-polymers00
Water73941
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area750 Å2
ΔGint-5 kcal/mol
Surface area3060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.595, 44.595, 41.865
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

-
Components

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


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


Mass: 18.015 Da / Num. of mol.: 41 / 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: 2.49 Å3/Da / Density % sol: 50.61 % / Description: rod
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 10% v/v MPD, 40mM Sodium cacodylate pH 7.0, 12mM Spermine tetra-HCl, 80mM NaCl

-
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: 1.5→30 Å / Num. obs: 7613 / % possible obs: 100 % / Redundancy: 18.2 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 18
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 10.7 % / Rmerge(I) obs: 0.435 / Mean I/σ(I) obs: 4 / Num. unique obs: 770 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4F4N

4f4n


Resolution: 1.501→28.387 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.46
RfactorNum. reflection% reflection
Rfree0.196 406 5.33 %
Rwork0.162 --
obs0.1638 7613 99.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.501→28.387 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 320 0 41 361
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007358
X-RAY DIFFRACTIONf_angle_d0.838548
X-RAY DIFFRACTIONf_dihedral_angle_d12.244152
X-RAY DIFFRACTIONf_chiral_restr0.03562
X-RAY DIFFRACTIONf_plane_restr0.00816
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5008-1.7180.2191090.16352389X-RAY DIFFRACTION98
1.718-2.16430.17511550.1752386X-RAY DIFFRACTION100
2.1643-28.39170.20361420.15592432X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 11.5561 Å / Origin y: 16.7512 Å / Origin z: 0.866 Å
111213212223313233
T0.1076 Å20.0069 Å2-0.0037 Å2-0.0965 Å20.0019 Å2--0.093 Å2
L1.8597 °2-1.5503 °2-1.1417 °2-1.7814 °21.0375 °2--1.9875 °2
S-0.0093 Å °-0.0812 Å °0.0861 Å °0.0373 Å °0.012 Å °-0.1121 Å °-0.0301 Å °-0.0097 Å °-0.0009 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