[English] 日本語
Yorodumi
- PDB-7bpf: Structure of L-threoninol nucleic acid - RNA complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7bpf
TitleStructure of L-threoninol nucleic acid - RNA complex
Components
  • L-aTNA (3'-(*GP*CP*AP*GP*CP*AP*GP*C)-1')
  • RNA (5'-R(*GP*CP*UP*GP*CP*(5BU)P*GP*C)-3')
KeywordsRNA/NUCLEIC ACID / Xeno nucleic acid / artificial nucleic acid / acyclic nucleic acid / L-threnoniol nucleic acid / RNA / RNA-NUCLEIC ACID complex
Function / homologyDNA / RNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.75 Å
AuthorsKamiya, Y. / Satoh, T. / Kodama, A. / Suzuki, T. / Uchiyama, S. / Kato, K. / Asanuma, H.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED) Japan
CitationJournal: Commun Chem / Year: 2020
Title: Intrastrand backbone-nucleobase interactions stabilize unwound right-handed helical structures of heteroduplexes of L-aTNA/RNA and SNA/RNA
Authors: Kamiya, Y. / Satoh, T. / Kodama, A. / Suzuki, T. / Murayama, K. / Kashida, H. / Uchiyama, S. / Kato, K. / Asanuma, H.
History
DepositionMar 22, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 25, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Derived calculations
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RNA (5'-R(*GP*CP*UP*GP*CP*(5BU)P*GP*C)-3')
B: RNA (5'-R(*GP*CP*UP*GP*CP*(5BU)P*GP*C)-3')
C: L-aTNA (3'-(*GP*CP*AP*GP*CP*AP*GP*C)-1')
D: L-aTNA (3'-(*GP*CP*AP*GP*CP*AP*GP*C)-1')


Theoretical massNumber of molelcules
Total (without water)9,7624
Polymers9,7624
Non-polymers00
Water37821
1
A: RNA (5'-R(*GP*CP*UP*GP*CP*(5BU)P*GP*C)-3')
C: L-aTNA (3'-(*GP*CP*AP*GP*CP*AP*GP*C)-1')


Theoretical massNumber of molelcules
Total (without water)4,8812
Polymers4,8812
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RNA (5'-R(*GP*CP*UP*GP*CP*(5BU)P*GP*C)-3')
D: L-aTNA (3'-(*GP*CP*AP*GP*CP*AP*GP*C)-1')


Theoretical massNumber of molelcules
Total (without water)4,8812
Polymers4,8812
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.996, 33.344, 54.055
Angle α, β, γ (deg.)90.00, 115.64, 90.00
Int Tables number5
Space group name H-MI121
Components on special symmetry positions
IDModelComponents
11C-201-

HOH

-
Components

#1: RNA chain RNA (5'-R(*GP*CP*UP*GP*CP*(5BU)P*GP*C)-3')


Mass: 2292.251 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain L-aTNA (3'-(*GP*CP*AP*GP*CP*AP*GP*C)-1')


Mass: 2588.968 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: L-threoninol nucleic acid / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 28% PEG 400, 0.1M HEPES (pH 7.5), 0.2M Calcium chloride

-
Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.75→28.5 Å / Num. obs: 8609 / % possible obs: 98.7 % / Redundancy: 4.3 % / CC1/2: 0.989 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.051 / Rrim(I) all: 0.079 / Net I/σ(I): 13.9
Reflection shellResolution: 1.75→1.78 Å / Rmerge(I) obs: 0.307 / Num. unique obs: 2064 / CC1/2: 0.944 / Rpim(I) all: 0.25 / Rrim(I) all: 0.397 / % possible all: 99.1

-
Processing

Software
NameVersionClassification
REFMAC5.8.0266refinement
XDSdata reduction
Aimlessdata scaling
AutoSolphasing
RefinementMethod to determine structure: MAD / Resolution: 1.75→20 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.939 / SU B: 12.841 / SU ML: 0.173 / Cross valid method: THROUGHOUT / ESU R: 0.267 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.288 383 4.5 %RANDOM
Rwork0.269 ---
obs0.27 8218 98.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.734 Å2
Baniso -1Baniso -2Baniso -3
1-0.74 Å20 Å24.67 Å2
2---3.81 Å20 Å2
3----0.97 Å2
Refinement stepCycle: 1 / Resolution: 1.75→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 294 356 21 671
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.017706
X-RAY DIFFRACTIONr_bond_other_d0.0060.021356
X-RAY DIFFRACTIONr_angle_refined_deg1.6552.089994
X-RAY DIFFRACTIONr_angle_other_deg14.463.024810
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0810.274
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02390
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02110
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.3354.789706
X-RAY DIFFRACTIONr_scbond_other3.2934.804651
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.0817.242911
X-RAY DIFFRACTIONr_long_range_B_refined4.93847.0341097
X-RAY DIFFRACTIONr_long_range_B_other4.93747.0351097
X-RAY DIFFRACTIONr_rigid_bond_restr1.24431062
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 27 -
Rwork0.297 597 -
obs--99.05 %

+
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