[English] 日本語
Yorodumi
- PDB-7l0z: Spinach variant bound to DFHBI-1T -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7l0z
TitleSpinach variant bound to DFHBI-1T
ComponentsRNA (69-MER)
KeywordsRNA / fluorescent / aptamer
Function / homologyChem-2ZY / : / PHOSPHATE ION / SPERMINE / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsTruong, L. / Trachman, R.J. / Ferre-D'Amare, A.R.
CitationJournal: Rna / Year: 2021
Title: Fluorogenic aptamers resolve the flexibility of RNA junctions using orientation-dependent FRET.
Authors: Jeng, S.C.Y. / Trachman III, R.J. / Weissenboeck, F. / Truong, L. / Link, K.A. / Jepsen, M.D.E. / Knutson, J.R. / Andersen, E.S. / Ferre-D'Amare, A.R. / Unrau, P.J.
History
DepositionDec 13, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
G: RNA (69-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,63912
Polymers22,3731
Non-polymers1,26611
Water97354
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2160 Å2
ΔGint-44 kcal/mol
Surface area12330 Å2
Unit cell
Length a, b, c (Å)150.564, 48.692, 30.612
Angle α, β, γ (deg.)90.000, 91.364, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11G-105-

MG

21G-109-

NA

-
Components

-
RNA chain , 1 types, 1 molecules G

#1: RNA chain RNA (69-MER)


Mass: 22373.242 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Non-polymers , 7 types, 65 molecules

#2: Chemical ChemComp-2ZY / (5Z)-5-(3,5-difluoro-4-hydroxybenzylidene)-2-methyl-3-(2,2,2-trifluoroethyl)-3,5-dihydro-4H-imidazol-4-one


Mass: 320.215 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H9F5N2O2
#3: Chemical ChemComp-SPM / SPERMINE


Mass: 202.340 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H26N4
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#7: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 50.94 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 40 mM Tris-HCl pH 7.5, 100 mM KCl, 1 mM MgCl2

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.105 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.105 Å / Relative weight: 1
ReflectionResolution: 2.01→75.26 Å / Num. obs: 14648 / % possible obs: 98.7 % / Redundancy: 5.3 % / Biso Wilson estimate: 46.31 Å2 / CC1/2: 0.999 / Net I/σ(I): 13.5
Reflection shellResolution: 2.01→2.07 Å / Num. unique obs: 1167 / CC1/2: 0.627 / % possible all: 92.1

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5OB3

5ob3


Resolution: 2.1→75.26 Å / SU ML: 0.2582 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.8783
RfactorNum. reflection% reflection
Rfree0.2324 1293 9.98 %
Rwork0.1959 --
obs0.1996 11686 98.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 66.07 Å2
Refinement stepCycle: LAST / Resolution: 2.1→75.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1483 75 54 1612
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00611724
X-RAY DIFFRACTIONf_angle_d1.11822665
X-RAY DIFFRACTIONf_chiral_restr0.0506345
X-RAY DIFFRACTIONf_plane_restr0.006871
X-RAY DIFFRACTIONf_dihedral_angle_d17.2425858
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.180.331460.2991308X-RAY DIFFRACTION98.91
2.18-2.280.28311450.26691259X-RAY DIFFRACTION99.29
2.28-2.40.30281410.25841302X-RAY DIFFRACTION99.18
2.4-2.550.25051470.23741309X-RAY DIFFRACTION98.91
2.55-2.750.2851390.2491267X-RAY DIFFRACTION98.53
2.75-3.030.32231400.26421298X-RAY DIFFRACTION98.97
3.03-3.470.26561380.21041276X-RAY DIFFRACTION97.79
3.47-4.370.20661500.17841322X-RAY DIFFRACTION99.26
4.37-75.260.1721470.13911321X-RAY DIFFRACTION98.19
Refinement TLS params.Method: refined / Origin x: -36.8152928881 Å / Origin y: 12.3705808217 Å / Origin z: -0.479627498632 Å
111213212223313233
T0.420948081066 Å20.0260468795674 Å2-0.0545975283894 Å2-0.236482955583 Å2-0.0149382859037 Å2--0.244261938933 Å2
L5.01072173497 °2-0.150228286574 °2-0.598431720792 °2-2.42095497899 °2-0.280314402507 °2--2.1857530096 °2
S-0.0722560140963 Å °-0.179569026511 Å °0.0709574158993 Å °0.290368139125 Å °0.0897809830997 Å °0.139898891319 Å °0.016607284078 Å °-0.149997906571 Å °-0.00115005845845 Å °
Refinement TLS groupSelection details: all

+
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