[English] 日本語
Yorodumi
- PDB-481d: CRYSTAL STRUCTURE OF A HEXITOL NUCLEIC ACID (HNA) DUPLEX AT 1.6A ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 481d
TitleCRYSTAL STRUCTURE OF A HEXITOL NUCLEIC ACID (HNA) DUPLEX AT 1.6A RESOLUTION
Components5'-H(*(6HG)P*(6HT)P*(6HG)P*(6HT)P*(6HA)P*(6HC)P*(6HA)P*(6HC))-3'
KeywordsDNA / HEXITOL NUCLEIC ACID / DNA ANALOGUE / DOUBLE HELIX
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.6 Å
AuthorsDeclercq, R. / Van Meervelt, L.
Citation
Journal: J.Am.Chem.Soc. / Year: 2002
Title: Crystal structure of double helical hexitol nucleic acids.
Authors: Declercq, R. / Van Aerschot, A. / Read, R.J. / Herdewijn, P. / Van Meervelt, L.
#1: Journal: Angew.Chem.Int.Ed.Engl. / Year: 1995
Title: 1',5'-Anhydrohexitol Nucleic Acids, a New Promising Antisense Construct
Authors: Van Aerschot, A. / Verheggen, I. / Hendrix, C. / Herdewijn, P.
#2: Journal: Acta Crystallogr.,Sect.C / Year: 1995
Title: 1',5'-Anhydro-2',3'-Dideoxy-2'-(Guanin-9-Yl)-D-Arabino Hexitol
Authors: Declercq, R. / Herdewijn, P. / Van Meervelt, L.
#3: Journal: J.Am.Chem.Soc. / Year: 1998
Title: Molecular Dynamics Simulation to Investigate Differences in Groove Hydration of HNA/RNA Hybrids as Compared to HNA/DNA Complexes
Authors: De Winter, H. / Lescrinier, E. / Van Aerschot, A. / Herdewijn, P
#4: Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Oligonucleotides with 1',5'-Anhydrohexitol Nucleoside Building Blocks: Crystallisation and Preliminary X-Ray Studies of h(GTGTACAC)
Authors: Declercq, R. / Van Aerschot, A. / Herdewijn, P. / Van Meervelt, L.
History
DepositionJul 23, 1999Deposition site: NDB / Processing site: NDB
Revision 1.0Apr 27, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 5'-H(*(6HG)P*(6HT)P*(6HG)P*(6HT)P*(6HA)P*(6HC)P*(6HA)P*(6HC))-3'


Theoretical massNumber of molelcules
Total (without water)2,5391
Polymers2,5391
Non-polymers00
Water72140
1
A: 5'-H(*(6HG)P*(6HT)P*(6HG)P*(6HT)P*(6HA)P*(6HC)P*(6HA)P*(6HC))-3'

A: 5'-H(*(6HG)P*(6HT)P*(6HG)P*(6HT)P*(6HA)P*(6HC)P*(6HA)P*(6HC))-3'


Theoretical massNumber of molelcules
Total (without water)5,0782
Polymers5,0782
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555x,x-y,-z1
Unit cell
Length a, b, c (Å)33.041, 33.041, 38.924
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number153
Cell settingtrigonal
Space group name H-MP3212

-
Components

#1: DNA chain 5'-H(*(6HG)P*(6HT)P*(6HG)P*(6HT)P*(6HA)P*(6HC)P*(6HA)P*(6HC))-3'


Mass: 2538.831 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: THE SUGAR MOIETIES ARE NOT DEOXYRIBOSE BUT D-ARABINO-HEXITOL
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 2.42 Å3/Da / Density % sol: 49.09 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7
Details: CRYSTALS WERE OBTAINED FROM A SOLUTION THAT CONTAINED CACODYLATE BUFFER, KCL, BACL2, SPERMINE TETRACHLORIDE, AND MPD, pH 7.0, VAPOR DIFFUSION, HANGING DROP
Components of the solutions
IDNameCrystal-IDSol-ID
1CACODYLATE BUFFER11
2KCL11
3BACL211
4SPERMINE11
5MPD11
6MPD12
Crystal grow
*PLUS
Temperature: 277 K
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
12.4 mMoligomer solution1drop
210 %(v/v)MPD1drop
312 mMspermine hydrochloride1drop
480 mM1dropK+
520 mM1dropBa+
640 mMcacodylate1droppH7.0
735 %(v/v)MPD1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8375
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 22, 1998
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8375 Å / Relative weight: 1
ReflectionResolution: 1.6→20 Å / Num. all: 3345 / Num. obs: 3345 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 8.5 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 13.2
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.173 / Mean I/σ(I) obs: 6.6 / % possible all: 100
Reflection
*PLUS
Lowest resolution: 20 Å / Rmerge(I) obs: 0.071
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.173

-
Processing

Software
NameClassification
BRUTEmodel building
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
BRUTEphasing
RefinementStarting model: 2.21A P 62 2 2 STRUCTURE OF H(GTGTACAC) (NDB CODE HD0002) WAS USED AS MODEL

Resolution: 1.6→20 Å / Num. parameters: 843 / Num. restraintsaints: 1426 / Cross valid method: FREE R / σ(F): 0
StereochEM target val spec case: ALL OTHER CHEMICALLY EQUIVALENT BOND DISTANCES AND ANGLES WERE RESTRAINED TO BE SIMILAR BY SAME DISTANCE RESTRAINTS
RfactorNum. reflection% reflectionSelection details
Rfree0.2287 325 9.8 %RANDOM
all0.1835 3330 --
obs0.1828 3330 99.9 %-
Solvent computationSolvent model: BULK SOLVENT MODELING: MOEWS & KRETSINGER, J.MOL.BIOL. 91, 201-228 (1973)
Refine analyzeOccupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 210
Refinement stepCycle: LAST / Resolution: 1.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 169 0 40 209
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.013
X-RAY DIFFRACTIONs_angle_d0.019
X-RAY DIFFRACTIONs_similar_dist0.046
X-RAY DIFFRACTIONs_from_restr_planes0.026
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.011
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.031
X-RAY DIFFRACTIONs_approx_iso_adps
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.1835 / Rfactor obs: 0.174 / Rfactor Rfree: 0.229 / Rfactor Rwork: 0.174
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://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