[English] 日本語
Yorodumi
- PDB-3t5e: Crystal structure of an intramolecular human telomeric DNA G-quad... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3t5e
TitleCrystal structure of an intramolecular human telomeric DNA G-quadruplex bound by the naphthalene diimide BMSG-SH-4
Componentshuman telomeric DNA sequence
KeywordsDNA / G-quadruplex / intramolecular / ligand-complex / telomeric
Function / homology: / Chem-T5E / DNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsCollie, G.W. / Promontorio, R. / Parkinson, G.N.
CitationJournal: J.Am.Chem.Soc. / Year: 2012
Title: Structural basis for telomeric g-quadruplex targeting by naphthalene diimide ligands.
Authors: Collie, G.W. / Promontorio, R. / Hampel, S.M. / Micco, M. / Neidle, S. / Parkinson, G.N.
History
DepositionJul 27, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: human telomeric DNA sequence
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,0145
Polymers6,9831
Non-polymers1,0314
Water68538
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.034, 63.034, 42.389
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6
Components on special symmetry positions
IDModelComponents
11A-26-

K

-
Components

#1: DNA chain human telomeric DNA sequence


Mass: 6983.497 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: DNA sequence synthesised by standard phosphoramidite chemistry
#2: Chemical ChemComp-T5E / 2,7-bis[4-(4-methylpiperazin-1-yl)butyl]-4,9-bis{[4-(4-methylpiperazin-1-yl)butyl]amino}benzo[lmn][3,8]phenanthroline-1 ,3,6,8(2H,7H)-tetrone / BMSG-SH2


Mass: 913.248 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C50H80N12O4
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 3.48 Å3/Da / Density % sol: 64.67 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 15% PEG400, 300 mM KBr, 50 mM sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 283K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 7, 2011
RadiationMonochromator: Si III channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.94→54.59 Å / Num. all: 7197 / Num. obs: 7197 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 8.9 % / Biso Wilson estimate: 42.15 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.2
Reflection shellResolution: 1.94→1.99 Å / Redundancy: 7 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 2 / Num. unique all: 531 / % possible all: 100

-
Processing

Software
NameVersionClassification
GDAdata collection
PHASERphasing
REFMAC5.5.0072refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1KF1

1kf1


Resolution: 2.1→10.2 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.935 / SU B: 9.672 / SU ML: 0.134 / Isotropic thermal model: Isotropic plus TLS / Cross valid method: THROUGHOUT / ESU R: 0.223 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28158 262 4.7 %RANDOM
Rwork0.24286 ---
all0.24474 5372 --
obs0.24474 5372 100 %-
Displacement parametersBiso mean: 40.688 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å2-0.06 Å20 Å2
2---0.12 Å20 Å2
3---0.19 Å2
Refinement stepCycle: LAST / Resolution: 2.1→10.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 465 69 38 572
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.021597
X-RAY DIFFRACTIONr_angle_refined_deg1.6222.999914
X-RAY DIFFRACTIONr_chiral_restr0.0550.287
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02272
X-RAY DIFFRACTIONr_scbond_it1.4653597
X-RAY DIFFRACTIONr_scangle_it2.3594.5914
LS refinement shellResolution: 2.1→2.152 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.448 15 -
Rwork0.385 373 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0016-0.00060.00010.0002-0.00010-0.4401-0.59310.94880.27090.24110.0693-0.7166-0.5570.19890.1236000.123600.1236-32.0347.3756-4.6732
20.0383-0.087-0.62110.19791.412210.0792-0.0118-0.30850.11880.31770.0804-0.15560.08240.2819-0.06850.1108-0.0017-0.00130.11220.00320.1354-26.06531.01551.5139
31.1106-3.09830.06718.6439-0.18720.00410.01520.2214-0.2858-0.24460.0211-0.61450.3820.5307-0.03640.1983-0.0062-0.00140.2132-0.00090.1955-17.7297-5.6219-11.1316
42.21290.86730.47960.5016-0.86016.8960.08080.32440.0534-0.4719-0.0705-0.0607-0.16960.0329-0.01030.1063-0.0068-0.00040.10760.00170.1394-28.64974.6698-17.9263
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 4
2X-RAY DIFFRACTION2A5 - 9
3X-RAY DIFFRACTION3A10 - 13
4X-RAY DIFFRACTION4A14 - 22

+
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