[English] 日本語
Yorodumi
- PDB-7eaf: Crystal structure of SAM-I riboswitch with the Actinomyces-1 k-turn -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7eaf
TitleCrystal structure of SAM-I riboswitch with the Actinomyces-1 k-turn
ComponentsRNA (94-MER)
KeywordsRNA / SAM / Riboswitch
Function / homology: / S-ADENOSYLMETHIONINE / RNA / RNA (> 10)
Function and homology information
Biological speciesCaldanaerobacter subterraneus subsp. tengcongensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsHuang, L. / Lilley, D.M.J.
Funding support China, United Kingdom, 2items
OrganizationGrant numberCountry
Ministry of Education (MoE, China) China
Cancer Research UKA18604 United Kingdom
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: Structure and folding of four putative kink turns identified in structured RNA species in a test of structural prediction rules.
Authors: Huang, L. / Liao, X. / Li, M. / Wang, J. / Peng, X. / Wilson, T.J. / Lilley, D.M.J.
History
DepositionMar 7, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 2, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 23, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 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 (94-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7659
Polymers30,5191
Non-polymers1,2458
Water905
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-10 kcal/mol
Surface area15030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.460, 61.460, 157.910
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-102-

BA

-
Components

#1: RNA chain RNA (94-MER)


Mass: 30519.307 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Caldanaerobacter subterraneus subsp. tengcongensis (bacteria)
#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Chemical
ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ba
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 2.44 Å3/Da / Density % sol: 49.65 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 40 MM NA-CACODYLATE (PH 7.0), 80 MM KCL, 40 MM BACL2, 12 MM SPERMINE-HCL, 12% (V/V) MPD.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 7963 / % possible obs: 99.6 % / Redundancy: 7.2 % / Biso Wilson estimate: 66.96 Å2 / CC1/2: 0.99 / Rpim(I) all: 0.056 / Rrim(I) all: 0.154 / Net I/σ(I): 8.9
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 7.7 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1123 / CC1/2: 0.771 / Rpim(I) all: 0.656 / % possible all: 99.6

-
Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5FK3

5fk3


Resolution: 2.85→29.22 Å / SU ML: 0.4498 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 45.4143
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2976 367 4.87 %
Rwork0.2621 7172 -
obs0.2639 7539 99.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 75.22 Å2
Refinement stepCycle: LAST / Resolution: 2.85→29.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2026 34 5 2065
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00422325
X-RAY DIFFRACTIONf_angle_d0.96533627
X-RAY DIFFRACTIONf_chiral_restr0.0438480
X-RAY DIFFRACTIONf_plane_restr0.006697
X-RAY DIFFRACTIONf_dihedral_angle_d15.90421154
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-3.260.36731060.30252330X-RAY DIFFRACTION98.82
3.26-4.110.28221210.2512346X-RAY DIFFRACTION98.8
4.11-29.220.29121400.25692496X-RAY DIFFRACTION99.4
Refinement TLS params.Method: refined / Origin x: -9.32676536 Å / Origin y: -9.95773684407 Å / Origin z: -23.0866878138 Å
111213212223313233
T0.725310504013 Å20.140789299773 Å20.0960715586856 Å2-0.592518506556 Å20.0863391107419 Å2--0.513179685662 Å2
L1.14406158049 °21.49978855029 °20.152405604736 °2-1.21493705298 °2-0.195771229289 °2--2.25907628295 °2
S-0.093813728766 Å °-0.147748414929 Å °0.226609401949 Å °-0.0766723219089 Å °0.260941565748 Å °-0.154801237559 Å °0.135245084704 Å °-0.00190368786849 Å °-0.146956928436 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