[English] 日本語
Yorodumi
- PDB-4l24: Crystal structure of metallo-DNA duplex containing consecutive T-... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4l24
TitleCrystal structure of metallo-DNA duplex containing consecutive T-Hg(II)-T base pairs
ComponentsDNA (5'-D(*CP*GP*CP*GP*AP*TP*TP*TP*CP*GP*CP*G)-3')
KeywordsDNA / metallo-DNA duplex / B-form DNA duplex / T-Hg(II)-T base pair / B-form double helix / Hg(II)
Function / homology: / DNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsKondo, J. / Yamada, T. / Hirose, C. / Okamoto, I. / Tanaka, Y. / Ono, A.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2014
Title: Crystal Structure of Metallo DNA Duplex Containing Consecutive Watson-Crick-like T-Hg(II) -T Base Pairs
Authors: Kondo, J. / Yamada, T. / Hirose, C. / Okamoto, I. / Tanaka, Y. / Ono, A.
History
DepositionJun 4, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 5, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: 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 / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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 / _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*TP*TP*TP*CP*GP*CP*G)-3')
B: DNA (5'-D(*CP*GP*CP*GP*AP*TP*TP*TP*CP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,7104
Polymers7,3092
Non-polymers4012
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-67 kcal/mol
Surface area4300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)25.500, 41.270, 64.560
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*TP*TP*TP*CP*GP*CP*G)-3')


Mass: 3654.378 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Chemically synthesized
#2: Chemical ChemComp-HG / MERCURY (II) ION / Mercury (element)


Mass: 200.590 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Hg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 2.32 Å3/Da / Density % sol: 47.07 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Sodium Cacodylate, Spermine tetrahydrochloride, 2-methyl-2,4-pentanediol, ammonium chloride, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1 Å
DetectorDate: Oct 16, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→34.8 Å / Num. obs: 2064

-
Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT3.11data extraction
CrystalCleardata reduction
CrystalCleardata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BNA

1bna


Resolution: 2.7→34.77 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.267 187 9 %
Rwork0.258 --
obs-2064 99.2 %
Solvent computationBsol: 42.01 Å2
Displacement parametersBiso max: 185.36 Å2 / Biso mean: 62.5829 Å2 / Biso min: 10.47 Å2
Baniso -1Baniso -2Baniso -3
1--1.457 Å20 Å20 Å2
2--37.106 Å20 Å2
3----35.65 Å2
Refinement stepCycle: LAST / Resolution: 2.7→34.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 484 2 14 500
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.16
X-RAY DIFFRACTIONc_mcbond_it01.5
X-RAY DIFFRACTIONc_scbond_it21.1542
X-RAY DIFFRACTIONc_mcangle_it20.2152
X-RAY DIFFRACTIONc_scangle_it20.3812.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7-2.80.8869170.8166180197100
2.8-2.910.011130.8338187200100
2.91-3.040.011160.5406180196100
3.04-3.20.011160.3212198214100
3.2-3.40.011120.2879178190100
3.4-3.660.011240.1891195219100
3.66-4.030.011140.2313189203100
4.03-4.620.011230.2189184207100
4.62-5.820.011250.2334192217100
5.82-1000.011270.260219422193.2
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1dna-rna_free.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param

+
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