[English] 日本語
Yorodumi
- PDB-1z3f: Structure of ellipticine in complex with a 6-bp DNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1z3f
TitleStructure of ellipticine in complex with a 6-bp DNA
Components5'-D(*CP*GP*AP*TP*CP*G)-3'
KeywordsDNA / ANTICANCER / DNA BINDING / DRUG DESIGN / ELLIPTICINE / INTERCALATOR
Function / homology: / ELLIPTICINE / DNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsCanals, A. / Purciolas, M. / Aymami, J. / Coll, M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2005
Title: The anticancer agent ellipticine unwinds DNA by intercalative binding in an orientation parallel to base pairs.
Authors: Canals, A. / Purciolas, M. / Aymami, J. / Coll, M.
History
DepositionMar 12, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 19, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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 / _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: 5'-D(*CP*GP*AP*TP*CP*G)-3'
B: 5'-D(*CP*GP*AP*TP*CP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,2907
Polymers3,6182
Non-polymers6715
Water48627
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)24.860, 24.860, 78.860
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

-
Components

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


Mass: 1809.217 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Chemical ChemComp-EL / ELLIPTICINE


Mass: 247.314 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H15N2 / Comment: alkaloid*YM
#3: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Co
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 1.62 Å3/Da / Density % sol: 23.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: MPD, sodium cacodylate, cobalt hexammine, sodium chloride, potassium chloride, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2sodium cacodylate11
3cobalt hexamine11
4sodium chloride11
5potassium chloride11
6H2O11
7MPD12
8sodium cacodylate12
9cobalt hexamine12
10potassium chloride12
11H2O12

-
Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 0.976 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 14, 2004 / Details: microfocus beamline
RadiationMonochromator: liq. N2 cooled Si-111 double monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.5→16.66 Å / Num. all: 4436 / Num. obs: 4420 / % possible obs: 99.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 1.5→1.54 Å / % possible all: 99.7

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
ProDCdata collection
XDSdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→16.66 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.971 / SU B: 6.257 / SU ML: 0.104 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.156 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24166 221 5 %RANDOM
Rwork0.22041 ---
all0.22 ---
obs0.2217 4197 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.952 Å2
Baniso -1Baniso -2Baniso -3
1-1.19 Å20.6 Å20 Å2
2--1.19 Å20 Å2
3----1.79 Å2
Refinement stepCycle: LAST / Resolution: 1.5→16.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 240 41 27 308
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.021312
X-RAY DIFFRACTIONr_angle_refined_deg2.5053476
X-RAY DIFFRACTIONr_chiral_restr0.0920.246
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.02162
X-RAY DIFFRACTIONr_nbd_refined0.1690.2107
X-RAY DIFFRACTIONr_nbtor_refined0.3350.2165
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2150.220
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1360.226
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0260.21
X-RAY DIFFRACTIONr_scbond_it4.0893590
X-RAY DIFFRACTIONr_scangle_it3.0534.5476
X-RAY DIFFRACTIONr_rigid_bond_restr8.4653590
X-RAY DIFFRACTIONr_sphericity_free6.374330
X-RAY DIFFRACTIONr_sphericity_bonded4.1973278
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 16 -
Rwork0.24 317 -
obs--100 %

+
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