[English] 日本語
Yorodumi
- PDB-3oz4: R-Methyl Carbocyclic LNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3oz4
TitleR-Methyl Carbocyclic LNA
ComponentsDNA (5'-D(*GP*CP*GP*TP*AP*(URX)P*AP*CP*GP*C)-3')
KeywordsDNA / A-form DNA / R-Methyl carbocyclic LNA / R-Me-c-LNA / antisense oligonucleotides
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å
AuthorsSeth, P.R. / Allerson, C.A. / Berdeja, A. / Siwkowski, A. / Pallan, P.S. / Gaus, H. / Prakash, T.P. / Watt, A.T. / Egli, M. / Swayze, E.E.
CitationJournal: J.Am.Chem.Soc. / Year: 2010
Title: An exocyclic methylene group acts as a bioisostere of the 2'-oxygen atom in LNA.
Authors: Seth, P.P. / Allerson, C.R. / Berdeja, A. / Siwkowski, A. / Pallan, P.S. / Gaus, H. / Prakash, T.P. / Watt, A.T. / Egli, M. / Swayze, E.E.
History
DepositionSep 24, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 24, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA (5'-D(*GP*CP*GP*TP*AP*(URX)P*AP*CP*GP*C)-3')
B: DNA (5'-D(*GP*CP*GP*TP*AP*(URX)P*AP*CP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)6,1422
Polymers6,1422
Non-polymers00
Water86548
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area980 Å2
ΔGint-2 kcal/mol
Surface area3800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)26.104, 43.491, 45.974
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(*GP*CP*GP*TP*AP*(URX)P*AP*CP*GP*C)-3')


Mass: 3071.043 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 42.1 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20 mM sodium cacodylate, 40 mM potassium chloride, 6 mM spermine tetrahydrochloride, 5% v/v MPD, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Components of the solutions
IDNameCrystal-IDSol-ID
1sodium cacodylate11
2potassium chloride11
3spermine tetrahydrochloride11
4MPD11
5sodium cacodylate12
6potassium chloride12
7spermine tetrahydrochloride12
8MPD12

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9782 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 12, 2009
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 0.9782 Å / Relative weight: 1
ReflectionResolution: 1.59→31.59 Å / Num. all: 7473 / Num. obs: 7451 / % possible obs: 99.7 % / Redundancy: 14 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 51.3
Reflection shellResolution: 1.59→1.65 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.527 / Mean I/σ(I) obs: 1.8 / Num. unique all: 714 / % possible all: 97.9

-
Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
CCP4model building
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3EY2

3ey2


Resolution: 1.59→31.59 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.95 / SU B: 3.854 / SU ML: 0.061 / Cross valid method: THROUGHOUT / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23686 559 7.5 %RANDOM
Rwork0.17239 ---
obs0.1771 6857 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.001 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å20 Å20 Å2
2---0.21 Å20 Å2
3---0.4 Å2
Refinement stepCycle: LAST / Resolution: 1.59→31.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 408 0 48 456
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.021454
X-RAY DIFFRACTIONr_angle_refined_deg2.1333692
X-RAY DIFFRACTIONr_chiral_restr0.1390.280
X-RAY DIFFRACTIONr_gen_planes_refined0.0260.02208
X-RAY DIFFRACTIONr_scbond_it3.8593454
X-RAY DIFFRACTIONr_scangle_it4.8754.5692
X-RAY DIFFRACTIONr_rigid_bond_restr2.9743454
LS refinement shellResolution: 1.59→1.632 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.402 31 -
Rwork0.294 492 -
obs--97.03 %

+
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