[English] 日本語
Yorodumi
- PDB-304d: SIDE-BY-SIDE BINDING OF DISTAMYCIN MOLECULES TO D(ICATATIC) IN TH... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 304d
TitleSIDE-BY-SIDE BINDING OF DISTAMYCIN MOLECULES TO D(ICATATIC) IN THE MONOCLINIC FORM
ComponentsDNA (5'-D(*IP*CP*AP*TP*AP*TP*IP*C)-3')
KeywordsDNA / B-DNA / DOUBLE HELIX / COMPLEXED WITH DRUG / DOUBLE DRUG IN THE MINOR GROOVE
Function / homologyDISTAMYCIN A / DNA
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsChen, X. / Ramakrishnan, B. / Sundaralingam, M.
Citation
Journal: J.Mol.Biol. / Year: 1997
Title: Crystal structures of the side-by-side binding of distamycin to AT-containing DNA octamers d(ICITACIC) and d(ICATATIC).
Authors: Chen, X. / Ramakrishnan, B. / Sundaralingam, M.
#1: Journal: Nat.Struct.Biol. / Year: 1994
Title: Binding of two Distamycin A Molecules in the Minor Groove of an Alternating B-DNA
Authors: Chen, X. / Ramakrishnan, B. / Rao, S.T. / Sundaralingam, M.
#2: Journal: Nat.Struct.Biol. / Year: 1995
Title: Crystal Structures of B-Form DNA-RNA Chimers Complexed with Distamycin
Authors: Chen, X. / Ramakrishnan, B. / Sundaralingam, M.
History
DepositionJan 3, 1997Deposition site: NDB / Processing site: NDB
Revision 1.0Sep 25, 1997Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA (5'-D(*IP*CP*AP*TP*AP*TP*IP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,8782
Polymers2,3971
Non-polymers4821
Water77543
1
A: DNA (5'-D(*IP*CP*AP*TP*AP*TP*IP*C)-3')
hetero molecules

A: DNA (5'-D(*IP*CP*AP*TP*AP*TP*IP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,7564
Polymers4,7932
Non-polymers9632
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Unit cell
Length a, b, c (Å)33.380, 25.330, 28.110
Angle α, β, γ (deg.)90.00, 120.45, 90.00
Int Tables number5
Space group name H-MC121

-
Components

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


Mass: 2396.589 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Chemical ChemComp-DMY / DISTAMYCIN A / DISTAMYCIN / STALLIMYCIN


Mass: 481.508 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H27N9O4 / Comment: antibiotic*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.06 Å3/Da / Density % sol: 40.15 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7 / Details: pH 7.00, VAPOR DIFFUSION, HANGING DROP / Temp details: ROOM TEMPERATURE
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3NA CACODYLATE11
4MGCL211
5SPERMINE_HCL11
6WATER12
7MPD12
Crystal grow
*PLUS
pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
11 mMDNA1dropsingle strand concentration
220 mMsodium cacodylate1drop
31 mMdistamycin hydrochloride1drop
420 mMmagnesium chloride1drop
51 mg/mlspermine hydrochloride1drop
63 %(v/v)MPD1drop
750 %1reservoir

-
Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE
DetectorType: SIEMENS-NICOLET / Detector: AREA DETECTOR / Date: Nov 3, 1994
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 1.6 Å / Num. all: 1770 / Num. obs: 1291 / % possible obs: 73 % / Observed criterion σ(I): 0 / Redundancy: 1.4 % / Rsym value: 0.014
Reflection
*PLUS
% possible obs: 73 % / Rmerge(I) obs: 0.014

-
Processing

Software
NameVersionClassification
XENGEN2data collection
XENGEN2data reduction
X-PLORrefinement
XENGENV. 2.0data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: GDHB25

Highest resolution: 1.9 Å / σ(F): 1
RfactorNum. reflection% reflection
Rwork0.184 --
obs0.184 1108 73 %
Displacement parametersBiso mean: 10.7 Å2
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Highest resolution: 1.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 159 35 43 237
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.018
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.8
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d37.2
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d5
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.9 Å / σ(F): 1
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 10.7 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg3.8
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg37.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg5

+
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