[English] 日本語
Yorodumi
- PDB-5do5: Crystal Structure of 2'-Fluoro-RNA bearing a phosphorodithioate -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5do5
TitleCrystal Structure of 2'-Fluoro-RNA bearing a phosphorodithioate
ComponentsRNA (5'-R(*CP*GP*CP*GP*AP*AP*UP*UP*(AF2)P*(2SG)P*CP*G)-3')
KeywordsRNA / 2'-fluoro-RNA / phosphorodithioate RNA / PS2-RNA
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsPallan, P.S. / Egli, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM086937 United States
CitationJournal: To Be Published
Title: Crystal Structure of 2'-Fluoro-RNA bearing a phosphorodithioate
Authors: Pallan, P.S. / Egli, M.
History
DepositionSep 10, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2016Group: Refinement description
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 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 (5'-R(*CP*GP*CP*GP*AP*AP*UP*UP*(AF2)P*(2SG)P*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)3,8871
Polymers3,8871
Non-polymers00
Water1,20767
1
A: RNA (5'-R(*CP*GP*CP*GP*AP*AP*UP*UP*(AF2)P*(2SG)P*CP*G)-3')

A: RNA (5'-R(*CP*GP*CP*GP*AP*AP*UP*UP*(AF2)P*(2SG)P*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)7,7752
Polymers7,7752
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area1190 Å2
ΔGint-2 kcal/mol
Surface area4510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.237, 34.366, 31.976
Angle α, β, γ (deg.)90.000, 127.500, 90.000
Int Tables number5
Space group name H-MC121
SymmetryPoint symmetry: (Schoenflies symbol: C (n fold cyclic))
Components on special symmetry positions
IDModelComponents
11A-234-

HOH

-
Components

#1: RNA chain RNA (5'-R(*CP*GP*CP*GP*AP*AP*UP*UP*(AF2)P*(2SG)P*CP*G)-3')


Mass: 3887.498 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 2.41 Å3/Da / Density % sol: 49.04 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: sodium cacodylate, pH 6.0, 40 mM sodium chloride, 10 mM magnesium chloride, 6 mM spermine tetrahydrochloride, and 5% v/v MPD

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 3, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.2→50 Å / Num. obs: 11122 / % possible obs: 99.3 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.032 / Rrim(I) all: 0.077 / Χ2: 1.854 / Net I/av σ(I): 44.679 / Net I/σ(I): 11.6 / Num. measured all: 62980
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.2-1.242.60.29310500.8750.2090.3610.75194
1.24-1.293.40.26611160.9110.1650.3140.87599.2
1.29-1.354.20.28810900.9510.150.3260.878100
1.35-1.425.60.31711320.9620.140.3470.927100
1.42-1.516.80.26911020.9740.1110.2911.13999.9
1.51-1.636.90.16411160.9880.0670.1771.592100
1.63-1.7970.1111300.9950.0450.1191.932100
1.79-2.056.90.08911150.9940.0370.0972.378100
2.05-2.596.70.07111210.9950.030.0772.915100
2.59-506.20.05311500.9950.0260.063.21699.6

-
Processing

Software
NameVersionClassification
SHELXrefinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID:2Q1R

2q1r


Resolution: 1.2→50 Å / WRfactor Rfree: 0.2297 / WRfactor Rwork: 0.19 / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2297 553 5 %Random
Rwork0.19 ---
obs-11102 99.3 %-
Displacement parametersBiso max: 152.45 Å2 / Biso mean: 19.0865 Å2 / Biso min: 7.02 Å2
Refinement stepCycle: LAST / Resolution: 1.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 255 0 67 322

+
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