[English] 日本語
Yorodumi
- PDB-188d: HYDRATION PATTERNS AND INTERMOLECULAR INTERACTIONS IN A-DNA CRYST... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 188d
TitleHYDRATION PATTERNS AND INTERMOLECULAR INTERACTIONS IN A-DNA CRYSTAL STRUCTURES. IMPLICATIONS FOR DNA RECOGNITION
ComponentsDNA (5'-D(*GP*GP*GP*CP*GP*CP*CP*C)-3')
KeywordsDNA / A-DNA / DOUBLE HELIX
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsEisenstein, M. / Shakked, Z.
Citation
Journal: J.Mol.Biol. / Year: 1995
Title: Hydration patterns and intermolecular interactions in A-DNA crystal structures. Implications for DNA recognition.
Authors: Eisenstein, M. / Shakked, Z.
#1: Journal: Acta Crystallogr.,Sect.B / Year: 1988
Title: Low-Temperature Study of the A-DNA Fragment d(GGGCGCCC)
Authors: Eisenstein, M. / Hope, H. / Haran, T.E. / Frolow, F. / Shakked, Z. / Rabinovich, D.
History
DepositionSep 2, 1994Deposition site: BNL / Processing site: NDB
Revision 1.0Feb 7, 1995Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA (5'-D(*GP*GP*GP*CP*GP*CP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)2,4291
Polymers2,4291
Non-polymers00
Water75742
1
A: DNA (5'-D(*GP*GP*GP*CP*GP*CP*CP*C)-3')

A: DNA (5'-D(*GP*GP*GP*CP*GP*CP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)4,8572
Polymers4,8572
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Unit cell
Length a, b, c (Å)42.740, 42.740, 24.570
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-26-

HOH

21A-37-

HOH

31A-50-

HOH

-
Components

#1: DNA chain DNA (5'-D(*GP*GP*GP*CP*GP*CP*CP*C)-3')


Mass: 2428.593 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.76 %
Crystal growTemperature: 292 K / Method: vapor diffusion / pH: 7 / Details: pH 7.00, VAPOR DIFFUSION, temperature 292.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3NA CACODYLATE11
4MGCL211
5WATER12
6MPD12
Crystal grow
*PLUS
Temperature: 115 K / Method: other
Details: Eisenstein, M., (1988) Acta Crystallogr.,Sect.B, 44, 625.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDChemical formula
130 %(v/v)MPD1
250 mMcacodylate1
315 mM1MgCl2
41
51
61

-
Data collection

DiffractionMean temperature: 115 K
Diffraction sourceSource: ROTATING ANODE
DetectorType: RIGAKU AFC-5 / Detector: DIFFRACTOMETER
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 1.7 Å
Reflection
*PLUS
Highest resolution: 1.7 Å

-
Processing

SoftwareName: NUCLSQ / Classification: refinement
RefinementResolution: 2.2→8 Å / σ(F): 2 /
RfactorNum. reflection
obs0.183 1524
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 2.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 161 0 42 203
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONn_bond_d0.0060.02
X-RAY DIFFRACTIONn_angle_d0.0160.04
X-RAY DIFFRACTIONn_planar_d
X-RAY DIFFRACTIONn_hb_or_metal_coord
X-RAY DIFFRACTIONn_sugar_bond_it1.3533
X-RAY DIFFRACTIONn_sugar_angle_it2.1275
X-RAY DIFFRACTIONn_phos_bond_it1.5933
X-RAY DIFFRACTIONn_phos_angle_it2.0875
X-RAY DIFFRACTIONn_bond_angle_restr
X-RAY DIFFRACTIONn_dihedral_angle_restr
X-RAY DIFFRACTIONn_impr_tor
X-RAY DIFFRACTIONn_sugar_bond_d
X-RAY DIFFRACTIONn_sugar_bond_angle_d
X-RAY DIFFRACTIONn_phos_bond_d0.0160.03
X-RAY DIFFRACTIONn_phos_bond_angle_d0.0380.06
X-RAY DIFFRACTIONn_plane_restr0.0050.02
X-RAY DIFFRACTIONn_chiral_restr0.0080.03
X-RAY DIFFRACTIONn_singtor_nbd0.1270.2
X-RAY DIFFRACTIONn_multtor_nbd0.120.2
X-RAY DIFFRACTIONn_xhyhbond_nbd
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 8 Å / σ(F): 2 / Rfactor obs: 0.183
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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