[English] 日本語
Yorodumi
- PDB-360d: STRUCTURE OF 2,5-BIS{[4-(N-ETHYLAMIDINO)PHENYL]}FURAN COMPLEXED T... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 360d
TitleSTRUCTURE OF 2,5-BIS{[4-(N-ETHYLAMIDINO)PHENYL]}FURAN COMPLEXED TO 5'-D(CPGPCPGPAPAPTPTPCPGPCPG)-3'. A MINOR GROOVE DRUG COMPLEX, SHOWING PATTERNS OF GROOVE HYDRATION
ComponentsDNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3')
KeywordsDNA / B-DNA / DOUBLE HELIX / COMPLEXED WITH DRUG
Function / homologyChem-BPF / DNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsGuerri, A. / Simpson, I.J. / Neidle, S.
CitationJournal: Nucleic Acids Res. / Year: 1998
Title: Visualisation of extensive water ribbons and networks in a DNA minor-groove drug complex.
Authors: Guerri, A. / Simpson, I.J. / Neidle, S.
History
DepositionOct 29, 1997Deposition site: NDB / Processing site: NDB
Revision 1.0Jul 16, 1998Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 25, 2012Group: Non-polymer description
Revision 1.4Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.5Apr 8, 2020Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.6Aug 2, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_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: DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3')
B: DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,7144
Polymers7,3272
Non-polymers3872
Water3,945219
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)24.240, 39.940, 65.880
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

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


Mass: 3663.392 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-BPF / N,N'-(furan-2,5-diylbis{benzene-4,1-diyl[(Z)-aminomethylylidene]})diethanaminium / DB185 / FURAMIDINE DERIVATIVE


Mass: 362.468 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H26N4O
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 219 / 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: 2.18 Å3/Da / Density % sol: 43.48 %
Crystal growTemperature: 288 K / Method: vapor diffusion / pH: 7 / Details: pH 7.00, VAPOR DIFFUSION, temperature 288.0K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2SODIUM CACODYLATE11
3SPERMINE11
4MGCL211
5MPD11
6WATER12
7MPD12
Crystal grow
*PLUS
Temperature: 15 ℃ / pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
23 mMdodecanucleotide1drop
310 mMspermine1drop
43 mMdrug1drop
575 mM1dropMgCl2
625 %(v/w)MPD1drop
730 %(v/w)1reservoir
1sodium cacodylate1drop

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Jul 1, 1997 / Details: MIRROR
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.85→7 Å / Num. obs: 5634 / % possible obs: 91.44 % / Observed criterion σ(I): 4 / Rmerge(I) obs: 0.022 / Net I/σ(I): 33.18
Reflection shellResolution: 1.854→1.9 Å / Mean I/σ(I) obs: 14.67 / % possible all: 80.7
Reflection
*PLUS
% possible obs: 96.2 % / Num. measured all: 36613 / Rmerge(I) obs: 0.034

-
Processing

Software
NameClassification
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NDB ENTRY GDL045 (PDB: 289D)

289d


Resolution: 1.85→7 Å / Num. parameters: 2904 / Num. restraintsaints: 3734 / Cross valid method: NONE / σ(F): 4
StereochEM target val spec case: STEREOCHEMISTRY OF LIGAND FROM MM CALCULATIONS
Stereochemistry target values: PARKINSON ET AL.
RfactorNum. reflection% reflection
Rwork0.166 --
all-5634 -
obs-5386 91.4 %
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-22
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 260 / Occupancy sum non hydrogen: 733
Refinement stepCycle: LAST / Resolution: 1.85→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 486 28 219 733
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.85 Å / Lowest resolution: 7 Å / σ(F): 4 / Rfactor obs: 0.169 / Rfactor Rfree: 0.227 / Rfactor Rwork: 0.17
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.009
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg0.023

+
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