[English] 日本語
Yorodumi
- PDB-5axf: Crystal Structure Analysis of DNA Duplexes containing sulfoamide-... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5axf
TitleCrystal Structure Analysis of DNA Duplexes containing sulfoamide-bridged nucleic acid (SuNA-NMe)
ComponentsDNA (5'-D(*GP*CP*GP*TP*AP*(LSM)P*AP*CP*GP*C)-3')
KeywordsDNA / A-FORM DNA / SULFONAMIDE-BRIDGED NUCLEIC ACID / SuNA[NMe] / ANTISENSE
Function / homologyDNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.13 Å
AuthorsMitsuoka, Y. / Aoyama, H. / Kugimiya, A. / Fujimura, Y. / Yamamoto, T. / Waki, R. / Wada, F. / Tahara, S. / Sawamura, M. / Noda, M. ...Mitsuoka, Y. / Aoyama, H. / Kugimiya, A. / Fujimura, Y. / Yamamoto, T. / Waki, R. / Wada, F. / Tahara, S. / Sawamura, M. / Noda, M. / Hari, Y. / Obika, S.
CitationJournal: Org.Biomol.Chem. / Year: 2016
Title: Effect of an N-substituent in sulfonamide-bridged nucleic acid (SuNA) on hybridization ability and duplex structure.
Authors: Mitsuoka, Y. / Aoyama, H. / Kugimiya, A. / Fujimura, Y. / Yamamoto, T. / Waki, R. / Wada, F. / Tahara, S. / Sawamura, M. / Noda, M. / Hari, Y. / Obika, S.
History
DepositionJul 28, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength
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*CP*GP*TP*AP*(LSM)P*AP*CP*GP*C)-3')
B: DNA (5'-D(*GP*CP*GP*TP*AP*(LSM)P*AP*CP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)6,3002
Polymers6,3002
Non-polymers00
Water2,360131
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area960 Å2
ΔGint-2 kcal/mol
Surface area3810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)24.420, 45.120, 45.450
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

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


Mass: 3150.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 1.9 Å3/Da / Density % sol: 35.23 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS AND I_PLUS/MINUS COLUMNS
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: MPD

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: May 14, 2014 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.13→32.02 Å / Num. obs: 19277 / % possible obs: 98.6 % / Redundancy: 6.8 % / Biso Wilson estimate: 8.06 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.025 / Net I/σ(I): 17.1 / Num. measured all: 131157 / Scaling rejects: 45
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.13-1.156.60.3784.664859860.9050.15798.3
6.08-32.024.30.03224.84471050.9980.01665.4

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
MOSFLM0.2.17data collection
Aimless0.2.17data scaling
PHASER2.5.6phasing
Cootmodel building
PHENIX1.9_1692refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.13→22.725 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 11.58 / Stereochemistry target values: ML
Details: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS AND I_PLUS/MINUS COLUMNS
RfactorNum. reflection% reflection
Rfree0.1448 1783 4.95 %
Rwork0.1305 34211 -
obs0.1312 19277 98.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 59.97 Å2 / Biso mean: 14.6927 Å2 / Biso min: 5.88 Å2
Refinement stepCycle: final / Resolution: 1.13→22.725 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 416 0 131 547
Biso mean---28.58 -
Num. residues----20
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.018560
X-RAY DIFFRACTIONf_angle_d2.096874
X-RAY DIFFRACTIONf_chiral_restr0.08194
X-RAY DIFFRACTIONf_plane_restr0.03224
X-RAY DIFFRACTIONf_dihedral_angle_d14.742250
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.1286-1.15910.21471330.17382699283299
1.1591-1.19320.17571650.151526052770100
1.1932-1.23170.15551760.136826472823100
1.2317-1.27580.15071410.124526432784100
1.2758-1.32680.13231410.123626772818100
1.3268-1.38720.12231350.123626922827100
1.3872-1.46030.13231460.109726482794100
1.4603-1.55180.13931290.108826742803100
1.5518-1.67160.14181400.098726632803100
1.6716-1.83970.11941280.103226792807100
1.8397-2.10580.14711030.123526782781100
2.1058-2.65240.14221440.150226882832100
2.6524-22.72960.1531020.15242218232083

+
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