[English] 日本語
Yorodumi
- PDB-5hix: Cocrystal structure of an anti-parallel DNA G-quadruplex and a te... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5hix
TitleCocrystal structure of an anti-parallel DNA G-quadruplex and a tetra-Quinoline Foldamer
ComponentsDimeric G-quadruplex
KeywordsDNA / DNA G-quadruplex / Foldamer / Foldamer-quadruplex / G-quadruplex Ligands
Function / homologyChem-61Q / : / DNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 Å
AuthorsMandal, P.K. / Baptiste, B. / Langlois d'Estaintot, B. / Kauffmann, B. / Huc, I.
Funding support France, 1items
OrganizationGrant numberCountry
European Research CouncilERC-2012-AdG-320892 France
CitationJournal: Chembiochem / Year: 2016
Title: Multivalent Interactions between an Aromatic Helical Foldamer and a DNA G-Quadruplex in the Solid State.
Authors: Mandal, P.K. / Baptiste, B. / Langlois d'Estaintot, B. / Kauffmann, B. / Huc, I.
History
DepositionJan 12, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 2, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Dimeric G-quadruplex
B: Dimeric G-quadruplex
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,7887
Polymers7,6112
Non-polymers1,1775
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3160 Å2
ΔGint-18 kcal/mol
Surface area4250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.701, 31.701, 97.373
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

-
Components

#1: DNA chain Dimeric G-quadruplex


Mass: 3805.460 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Oxytricha Nova / Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-61Q / 4-(3-aminopropoxy)-8-({[4-(3-aminopropoxy)-8-({[4-(3-aminopropoxy)-8-({[4-(3-aminopropoxy)-8-nitroquinolin-2-yl]carbonyl}amino)quinolin-2-yl]carbonyl}amino)quinolin-2-yl]carbonyl}amino)quinoline-2-carboxylic acid


Mass: 1021.043 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C52H52N12O11
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: d(GGGGTTTTGGGG), 8-amino-2-quinolinecarboxylic acid, potassium cacodylate, magnesium chloride, potassium chloride, spermine, 2-methyl-2,4-pentanediol (MPD)
PH range: 7

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 7, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.519
11-H, K, -L20.481
ReflectionResolution: 2.48→30.14 Å / Num. obs: 3345 / % possible obs: 97.72 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.06
Reflection shellResolution: 2.48→2.57 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.87 / Mean I/σ(I) obs: 1.95 / % possible all: 88.62

-
Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
XDSdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JRN

1jrn


Resolution: 2.48→30.14 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.918 / SU B: 18.537 / SU ML: 0.387 / Cross valid method: THROUGHOUT / ESU R: 0.108 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28784 157 4.7 %RANDOM
Rwork0.22694 ---
obs0.23052 3151 96.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.927 Å2
Baniso -1Baniso -2Baniso -3
1-31.99 Å20 Å20 Å2
2--31.99 Å20 Å2
3----63.98 Å2
Refinement stepCycle: 1 / Resolution: 2.48→30.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 506 79 10 595
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.012650
X-RAY DIFFRACTIONr_bond_other_d0.0150.021329
X-RAY DIFFRACTIONr_angle_refined_deg1.6681.341994
X-RAY DIFFRACTIONr_angle_other_deg3.563.065772
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0840.272
X-RAY DIFFRACTIONr_gen_planes_refined0.0190.021375
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02127
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it6.4675.759650
X-RAY DIFFRACTIONr_scbond_other6.4635.768651
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.2968.601995
X-RAY DIFFRACTIONr_long_range_B_refined12.65162.0441225
X-RAY DIFFRACTIONr_long_range_B_other12.64762.1051225
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.481→2.545 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.516 6 -
Rwork0.309 192 -
obs--78.57 %

+
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