[English] 日本語
Yorodumi
- PDB-5ccw: Structure of the complex of a human telomeric DNA with Au(caffein... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ccw
TitleStructure of the complex of a human telomeric DNA with Au(caffein-2-ylidene)2
Componentshuman telomeric DNA
KeywordsDRUG/DNA / DRUG-DNA COMPLEX / G-QUADRUPLEX
Function / homologyAu(caffein-2-ylidene)2 / : / DNA / DNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.89 Å
AuthorsFerraroni, M. / Bazzicalupi, C. / Gratteri, P. / Messori, L. / Papi, F.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2016
Title: Determinants for Tight and Selective Binding of a Medicinal Dicarbene Gold(I) Complex to a Telomeric DNA G-Quadruplex: a Joint ESI MS and XRD Investigation.
Authors: Bazzicalupi, C. / Ferraroni, M. / Papi, F. / Massai, L. / Bertrand, B. / Messori, L. / Gratteri, P. / Casini, A.
History
DepositionJul 2, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 16, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 30, 2016Group: Database references
Revision 1.2Jan 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.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: human telomeric DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,2066
Polymers7,2881
Non-polymers1,9185
Water39622
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.129, 51.286, 58.768
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11A-103-

51O

21A-213-

HOH

-
Components

#1: DNA chain human telomeric DNA


Mass: 7287.690 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-51O / Au(caffein-2-ylidene)2


Mass: 613.401 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C18H24AuN8O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 2.44 Å3/Da / Density % sol: 49.52 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: PEG400, lithium sulphate, sodium cacodylate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9798 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 1.89→38.64 Å / Num. all: 5821 / Num. obs: 5821 / % possible obs: 97.8 % / Redundancy: 12.8 % / Rsym value: 0.069 / Net I/σ(I): 15.36
Reflection shellResolution: 1.89→2.01 Å / Redundancy: 8.7 % / Rmerge(I) obs: 0.117 / Mean I/σ(I) obs: 1.6 / % possible all: 87.7

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2 Å36.73 Å
Translation2 Å36.73 Å

-
Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
PHASER2.5.6phasing
PDB_EXTRACT3.15data extraction
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3R6R

3r6r


Resolution: 1.89→30 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.973 / WRfactor Rfree: 0.2589 / WRfactor Rwork: 0.215 / FOM work R set: 0.6627 / SU B: 6.89 / SU ML: 0.178 / SU R Cruickshank DPI: 0.1763 / SU Rfree: 0.1584 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.176 / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2601 295 5.1 %RANDOM
Rwork0.2253 ---
obs0.2271 5512 97.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 124.63 Å2 / Biso mean: 46.575 Å2 / Biso min: 25.89 Å2
Baniso -1Baniso -2Baniso -3
1-3.84 Å20 Å2-0 Å2
2---6.32 Å20 Å2
3---2.49 Å2
Refinement stepCycle: final / Resolution: 1.89→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 426 95 22 543
Biso mean--35.68 46.27 -
Num. residues----21
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.012581
X-RAY DIFFRACTIONr_angle_refined_deg1.1331.467904
X-RAY DIFFRACTIONr_chiral_restr0.0690.261
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02310
X-RAY DIFFRACTIONr_scbond_it3.9114.776580
LS refinement shellResolution: 1.892→1.941 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.652 19 -
Rwork0.488 308 -
all-327 -
obs--78.23 %

+
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