[English] 日本語
Yorodumi
- PDB-7jjf: Sarcin-ricin loop with modified residue. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7jjf
TitleSarcin-ricin loop with modified residue.
ComponentsRNA/DNA (27-mer)
KeywordsDNA-RNA HYBRID / sarcin-ricin loop / RNA crystal structure / RNA tetraloops / RNA
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsHarp, J.M. / Pallan, P.S. / Egli, M.
CitationJournal: Biochemistry / Year: 2020
Title: Incorporating a Thiophosphate Modification into a Common RNA Tetraloop Motif Causes an Unanticipated Stability Boost.
Authors: Pallan, P.S. / Lybrand, T.P. / Schlegel, M.K. / Harp, J.M. / Jahns, H. / Manoharan, M. / Egli, M.
History
DepositionJul 25, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2020Provider: 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
A: RNA/DNA (27-mer)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,7512
Polymers8,7261
Non-polymers241
Water1,856103
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)29.340, 29.340, 75.661
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43
Symmetry operation#1: x,y,z
#2: -y,x,z+3/4
#3: y,-x,z+1/4
#4: -x,-y,z+1/2

-
Components

#1: RNA chain RNA/DNA (27-mer)


Mass: 8726.282 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.81 Å3/Da / Density % sol: 32.06 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: RNA was dissolved in 1 mM Na2 EDTA (pH 8.0) and 10 mM Tris-HCl (pH 8.0) to attain 350 uM final RNA concentration. The RNA sample was annealed by heating at 65 C for 2 min and slowly cooling ...Details: RNA was dissolved in 1 mM Na2 EDTA (pH 8.0) and 10 mM Tris-HCl (pH 8.0) to attain 350 uM final RNA concentration. The RNA sample was annealed by heating at 65 C for 2 min and slowly cooling to room temperature. Crystallization set-ups were made by mixing 4 uL of RNA solution with 2 uL of a crystallization buffer composed of 3.0 M ammonium sulfate, 10 mM magnesium chloride, 10 mM manganese chloride, and 50 mM potassium 3-(N-morpholino) propanesulfonic acid (MOPS), pH 7.0 at 18 C. Crystals appear in about two weeks time.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: LIQUID ANODE / Type: Excillum MetalJet D2+ 70 kV / Wavelength: 1.3418 Å
DetectorType: Bruker PHOTON III / Detector: PIXEL / Date: Mar 19, 2020
RadiationMonochromator: multi-layer confocal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3418 Å / Relative weight: 1
ReflectionResolution: 1.2→27.36 Å / % possible obs: 94.1 % / Redundancy: 17 % / Biso Wilson estimate: 4.79 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 23.47
Reflection shellResolution: 1.2→1.24 Å

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PROTEUM PLUSdata reduction
PROTEUM PLUSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DVZ

3dvz


Resolution: 1.2→27.36 Å / Cross valid method: FREE R-VALUE / σ(F): 4.58 / Phase error: 41.508
Stereochemistry target values: GEOSTD + MONOMER LIBRARY + CDL V1.2
RfactorNum. reflection% reflection
Rfree0.214 3874 10.65 %
Rwork0.177 --
obs0.184 36363 92.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 10.76 Å2
Refinement stepCycle: LAST / Resolution: 1.2→27.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 578 1 103 682
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007675
X-RAY DIFFRACTIONf_angle_d1.3421049
X-RAY DIFFRACTIONf_dihedral_angle_d15.367351
X-RAY DIFFRACTIONf_chiral_restr0.054140
X-RAY DIFFRACTIONf_plane_restr0.00928
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.220.37831570.34451320X-RAY DIFFRACTION64
1.22-1.240.34461470.33411262X-RAY DIFFRACTION67
1.24-1.270.39841520.31161361X-RAY DIFFRACTION67
1.27-1.290.31131550.29991405X-RAY DIFFRACTION73
1.29-1.320.37041640.31341476X-RAY DIFFRACTION74
1.32-1.350.31191730.29141445X-RAY DIFFRACTION73
1.35-1.390.27961870.27531590X-RAY DIFFRACTION80
1.39-1.420.24741950.25361645X-RAY DIFFRACTION84
1.42-1.460.28681910.22661705X-RAY DIFFRACTION87
1.46-1.510.23761870.20381737X-RAY DIFFRACTION88
1.51-1.570.22151900.18461762X-RAY DIFFRACTION89
1.57-1.630.19042040.15531792X-RAY DIFFRACTION90
1.63-1.70.16852040.14941742X-RAY DIFFRACTION89
1.7-1.790.17231980.15211766X-RAY DIFFRACTION90
1.79-1.90.18072060.14321764X-RAY DIFFRACTION90
1.9-2.050.20581940.15411789X-RAY DIFFRACTION90
2.05-2.260.16992030.14761800X-RAY DIFFRACTION90
2.26-2.580.1571980.14551740X-RAY DIFFRACTION90
2.59-3.250.18422030.13761794X-RAY DIFFRACTION90
3.26-29.340.18731900.13831770X-RAY DIFFRACTION90

+
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