[English] 日本語
Yorodumi
- PDB-5kvj: Crystal structure of the 16-mer doublestranded RNA. Northeast Str... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5kvj
TitleCrystal structure of the 16-mer doublestranded RNA. Northeast Structural Genomics Consortium (NESG) target RNA1
Components
  • RNA (5'-R(P*CP*CP*AP*UP*CP*CP*UP*CP*UP*AP*CP*AP*GP*GP*CP*G)-3')
  • RNA (5'-R(P*CP*GP*CP*CP*UP*GP*UP*AP*GP*AP*GP*GP*AP*UP*GP*G)-3')
KeywordsRNA / double stranded RNA / dsRNA / Northeast Structural Genomics Consortium / NESG / PSI-Biology
Function / homologyARGININE / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.261 Å
AuthorsVorobiev, S.M. / Ma, L.-C. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be published
Title: Crystal structure of the 16-mer double stranded RNA.
Authors: Vorobiev, S.M. / Ma, L.-C. / Montelione, G.T.
History
DepositionJul 14, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RNA (5'-R(P*CP*CP*AP*UP*CP*CP*UP*CP*UP*AP*CP*AP*GP*GP*CP*G)-3')
B: RNA (5'-R(P*CP*GP*CP*CP*UP*GP*UP*AP*GP*AP*GP*GP*AP*UP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,4013
Polymers10,2262
Non-polymers1751
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1600 Å2
ΔGint-3 kcal/mol
Surface area6210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.299, 43.299, 124.441
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-207-

HOH

-
Components

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


Mass: 5033.047 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: RNA chain RNA (5'-R(P*CP*GP*CP*CP*UP*GP*UP*AP*GP*AP*GP*GP*AP*UP*GP*G)-3')


Mass: 5193.144 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-ARG / ARGININE


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N4O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.13 Å3/Da / Density % sol: 42.15 %
Crystal growTemperature: 291 K / Method: microbatch under paraffin oil / pH: 9
Details: 2.4 M Ammonium sulfate, 0.1 M BICINE, pH 9.0, dsRNA buffer: 0.025M NH4OAc, pH 5.5, 0.275 M NaCl, 0.005 M CaCl2, 0.001 M EDTA, 0.001 M TCEP, 0.025 M Arg, and 0.02% NaN3
PH range: 7.0-9.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 5, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.26→50 Å / Num. obs: 3824 / % possible obs: 93.6 % / Redundancy: 2 % / Rmerge(I) obs: 0.028 / Net I/σ(I): 37.2
Reflection shellResolution: 2.26→2.3 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.334 / Mean I/σ(I) obs: 3.5 / % possible all: 97.7

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3nd3

3nd3


Resolution: 2.261→21.649 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 28.14
RfactorNum. reflection% reflection
Rfree0.2334 189 4.97 %
Rwork0.1937 --
obs0.1958 3802 93.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.261→21.649 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12 682 0 10 704
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01771
X-RAY DIFFRACTIONf_angle_d1.3411193
X-RAY DIFFRACTIONf_dihedral_angle_d9.923384
X-RAY DIFFRACTIONf_chiral_restr0.054161
X-RAY DIFFRACTIONf_plane_restr0.05434
LS refinement shellResolution: 2.2605→21.6505 Å
RfactorNum. reflection% reflection
Rfree0.2334 189 -
Rwork0.1937 3613 -
obs--93 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.1913-2.17845.6075.18340.50023.97550.23490.0358-0.65910.1630.0890.38790.6121-0.3399-0.30420.4864-0.13140.05420.41740.05090.57897.996816.27262.8187
25.7613-1.94763.09822.6827-5.63765.57730.307-0.2554-0.532-0.11330.1410.33570.561-0.0444-0.4970.5378-0.0897-0.03460.4412-0.09780.646310.012114.96847.732
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

+
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