[English] 日本語
Yorodumi
- PDB-7xhd: Crystal structure of a dimeric interlocked parallel G-quadruplex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7xhd
TitleCrystal structure of a dimeric interlocked parallel G-quadruplex
ComponentsDNA (5'-D(*GP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*TP*GP*GP*GP*T)-3')
KeywordsDNA / G-quadruplex / interlocked
Function / homology: / DNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å
AuthorsNgo, K.H. / Liew, C.W. / Lattmann, S. / Winnerdy, F.R. / Phan, A.T.
Funding support Singapore, 2items
OrganizationGrant numberCountry
National Research Foundation (NRF, Singapore)NRF-NRFI2017-09 Singapore
Ministry of Education (MoE, Singapore)MOE2018-T2-2-029 Singapore
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2022
Title: Crystal structures of an HIV-1 integrase aptamer: Formation of a water-mediated A•G•G•G•G pentad in an interlocked G-quadruplex.
Authors: Ngo, K.H. / Liew, C.W. / Lattmann, S. / Winnerdy, F.R. / Phan, A.T.
History
DepositionApr 8, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 15, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA (5'-D(*GP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*TP*GP*GP*GP*T)-3')
B: DNA (5'-D(*GP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*TP*GP*GP*GP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,4407
Polymers10,2452
Non-polymers1955
Water1,78399
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)29.403, 30.917, 31.584
Angle α, β, γ (deg.)98.185, 97.150, 109.125
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

-
Components

#1: DNA chain DNA (5'-D(*GP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*TP*GP*GP*GP*T)-3')


Mass: 5122.284 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 2.58 Å3/Da / Density % sol: 52.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.002 M Copper(II) chloride dihydrate, 0.05 M TRIS hydrochloride pH 8.5, 1.8 M Lithium sulfate monohydrate, 0.0005 M Spermine

-
Data collection

DiffractionMean temperature: 90 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953659 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 19, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953659 Å / Relative weight: 1
ReflectionResolution: 1.66→24.54 Å / Num. obs: 11663 / % possible obs: 96.23 % / Redundancy: 3.6 % / Biso Wilson estimate: 21.13 Å2 / CC1/2: 0.998 / Net I/σ(I): 9.76
Reflection shellResolution: 1.66→1.72 Å / Num. unique obs: 1117 / CC1/2: 0.935

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
XDSdata reduction
PHENIX1.19.2_4158phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7XDH

7xdh


Resolution: 1.66→24.54 Å / SU ML: 0.1489 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 25.3003
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2116 1172 10.08 %
Rwork0.182 10455 -
obs0.185 11627 96.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.89 Å2
Refinement stepCycle: LAST / Resolution: 1.66→24.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 682 5 99 786
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076768
X-RAY DIFFRACTIONf_angle_d0.97961192
X-RAY DIFFRACTIONf_chiral_restr0.0462126
X-RAY DIFFRACTIONf_plane_restr0.008632
X-RAY DIFFRACTIONf_dihedral_angle_d31.8931312
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.66-1.740.2461420.22411256X-RAY DIFFRACTION91.97
1.74-1.830.24691470.23041299X-RAY DIFFRACTION95.57
1.83-1.940.24011440.20461293X-RAY DIFFRACTION96.31
1.94-2.090.24921470.19671317X-RAY DIFFRACTION96.7
2.09-2.30.24331460.20631304X-RAY DIFFRACTION97.38
2.3-2.630.21911460.20191347X-RAY DIFFRACTION97.45
2.64-3.320.25941540.21521308X-RAY DIFFRACTION96.95
3.32-24.540.1511460.13451331X-RAY DIFFRACTION97.88
Refinement TLS params.Method: refined / Origin x: -0.614512080543 Å / Origin y: -2.66999630187 Å / Origin z: 14.6700661252 Å
111213212223313233
T0.235572382628 Å2-0.00470339861743 Å20.00163292379396 Å2-0.233993677641 Å20.0141327562983 Å2--0.223933528982 Å2
L0.758724335676 °2-0.44829605353 °2-0.152306372666 °2-0.45931515329 °2-0.15428566813 °2--0.418665431008 °2
S-0.0391509769419 Å °0.0309479476835 Å °-0.027608475203 Å °0.0134730450774 Å °0.0121461446721 Å °-0.0370070627909 Å °0.039441484923 Å °-0.0127919038868 Å °-5.75474896611E-5 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://pdbjlvh1.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