[English] 日本語
Yorodumi
- PDB-224d: DNA-DRUG REFINEMENT: A COMPARISON OF THE PROGRAMS NUCLSQ, PROLSQ,... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 224d
TitleDNA-DRUG REFINEMENT: A COMPARISON OF THE PROGRAMS NUCLSQ, PROLSQ, SHELXL93 AND X-PLOR, USING THE LOW TEMPERATURE D(TGATCA)-NOGALAMYCIN STRUCTURE
ComponentsDNA (5'-D(*TP*GP*AP*TP*CP*A)-3')
KeywordsDNA / RIGHT HANDED DNA / DOUBLE HELIX / COMPLEXED WITH DRUG
Function / homologyNOGALAMYCIN / DNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 1.4 Å
AuthorsSchuerman, G.S. / Smith, C.K. / Turkenburg, J.P. / Dettmar, A.N. / Van Meervelt, L. / Moore, M.H.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1996
Title: DNA-drug refinement: a comparison of the programs NUCLSQ, PROLSQ, SHELXL93 and X-PLOR, using the low-temperature d(TGATCA)-nogalamycin structure.
Authors: Schuerman, G.S. / Smith, C.K. / Turkenburg, J.P. / Dettmar, A.N. / Van Meervelt, L. / Moore, M.H.
#1: Journal: Biochemistry / Year: 1995
Title: DNA-Nogalamycin Interactions: The Crystal Structure of d(TGATCA) Complexed with Nogalamycin
Authors: Smith, C.K. / Davies, G.J. / Dodson, E.J. / Moore, M.H.
History
DepositionAug 1, 1995Deposition site: BNL / Processing site: NDB
Revision 1.0Nov 14, 1995Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_special_symmetry / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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(*TP*GP*AP*TP*CP*A)-3')
B: DNA (5'-D(*TP*GP*AP*TP*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,1924
Polymers3,6162
Non-polymers1,5762
Water1,38777
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.290, 37.290, 71.120
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-90-

HOH

-
Components

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


Mass: 1808.229 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Chemical ChemComp-NGM / NOGALAMYCIN


Mass: 787.803 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C39H49NO16 / Comment: antitumor, antibiotic*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.42 Å3/Da / Density % sol: 64.02 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 6.5 / Details: pH 6.50, VAPOR DIFFUSION, SITTING DROP
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2HMD11
3SPERMINE11
4MGCL211
5NA CACODYLATE11
6WATER12
7MPD12
Crystal grow
*PLUS
pH: 6.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11.5 mMoligonucleotide1drop
22.7 mMnogalamycin1drop
35 %1,6-hexanediol1drop
41 mMspermine1drop
517 mM1dropMgCl2
6sodium cacodylate1drop
7100 %1reservoir

-
Data collection

DiffractionMean temperature: 150 K
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNum. obs: 9852
Reflection
*PLUS
Highest resolution: 1.4 Å
Reflection shell
*PLUS
Highest resolution: 1.4 Å / Lowest resolution: 1.47 Å / Num. unique obs: 1466 / Num. measured obs: 4641 / Rmerge(I) obs: 0.213

-
Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 1.4→8 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.274 --
obs0.228 9813 95.6 %
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 1.4→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 240 115 77 432
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr0.0310.02
X-RAY DIFFRACTIONp_chiral_restr0.1290.15
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd0.2730.5
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Highest resolution: 1.4 Å / Lowest resolution: 8 Å / σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: p_bond_d

+
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