[English] 日本語
Yorodumi
- PDB-6yml: Crystal structure of the SAM-SAH riboswitch with decarboxylated SAH -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6yml
TitleCrystal structure of the SAM-SAH riboswitch with decarboxylated SAH
Components
  • Chains: A,C
  • Chains: B,D
KeywordsRNA / Pseudoknot / SAM / Riboswitch
Function / homologyADENOSINE MONOPHOSPHATE / 5'-S-(3-aminopropyl)-5'-thioadenosine / RNA / RNA (> 10)
Function and homology information
Biological speciesRoseobacter sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.17 Å
AuthorsHuang, L. / Lilley, D.M.J.
Funding support United Kingdom, China, 2items
OrganizationGrant numberCountry
Cancer Research UKA18604 United Kingdom
Ministry of Education (MoE, China) China
CitationJournal: Nucleic Acids Res. / Year: 2020
Title: Crystal structure and ligand-induced folding of the SAM/SAH riboswitch.
Authors: Huang, L. / Liao, T.W. / Wang, J. / Ha, T. / Lilley, D.M.J.
History
DepositionApr 8, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 24, 2024Group: 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: Chains: A,C
B: Chains: B,D
C: Chains: A,C
D: Chains: B,D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6958
Polymers22,5714
Non-polymers1,1244
Water905
1
A: Chains: A,C
B: Chains: B,D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,0695
Polymers11,2862
Non-polymers7843
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Chains: A,C
D: Chains: B,D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,6263
Polymers11,2862
Non-polymers3401
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.218, 86.218, 75.395
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number149
Space group name H-MP312
Space group name HallP32
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: -y,-x,-z
#5: -x+y,y,-z
#6: x,x-y,-z

-
Components

-
RNA chain , 2 types, 4 molecules ACBD

#1: RNA chain Chains: A,C


Mass: 8389.874 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Roseobacter sp. (bacteria)
#2: RNA chain Chains: B,D


Mass: 2895.791 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Roseobacter sp. (bacteria)

-
Non-polymers , 4 types, 9 molecules

#3: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#4: Chemical ChemComp-DSH / 5'-S-(3-aminopropyl)-5'-thioadenosine


Mass: 340.401 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H20N6O3S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.72 Å3/Da / Density % sol: 66.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.01 M Magnesium Sulfate, 0.05 M Sodium Cacodylate pH 6.0, 1.8 M Lithium Sulfate monohydrate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9188 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9188 Å / Relative weight: 1
ReflectionResolution: 2.17→75.4 Å / Num. obs: 17121 / % possible obs: 100 % / Observed criterion σ(I): 0.6 / Redundancy: 9.7 % / Biso Wilson estimate: 69.42 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.033 / Net I/σ(I): 9.4
Reflection shellResolution: 2.17→2.2 Å / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 867 / CC1/2: 0.355 / Rpim(I) all: 1 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PHENIX1.17.1_3660refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6YL5

6yl5


Resolution: 2.17→53.05 Å / SU ML: 0.3452 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.1866
RfactorNum. reflection% reflection
Rfree0.2332 725 4.23 %
Rwork0.1983 --
obs0.1998 17121 99.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 74.95 Å2
Refinement stepCycle: LAST / Resolution: 2.17→53.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1484 70 5 1559
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00661731
X-RAY DIFFRACTIONf_angle_d1.48852683
X-RAY DIFFRACTIONf_chiral_restr0.1262356
X-RAY DIFFRACTIONf_plane_restr0.010673
X-RAY DIFFRACTIONf_dihedral_angle_d17.548857
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.17-2.330.35361260.2993156X-RAY DIFFRACTION96.13
2.33-2.570.39891720.31923230X-RAY DIFFRACTION100
2.57-2.940.36781410.33473318X-RAY DIFFRACTION100
2.94-3.70.28641300.22433317X-RAY DIFFRACTION100
3.7-53.050.1731560.14753375X-RAY DIFFRACTION99.97
Refinement TLS params.Method: refined / Origin x: 20.5268773692 Å / Origin y: -28.5433780996 Å / Origin z: 17.9665400538 Å
111213212223313233
T0.792646920848 Å2-0.0282211245561 Å2-0.00305360737992 Å2-0.611988832929 Å20.0299842351869 Å2--0.75943010969 Å2
L-0.602024258174 °20.181644062808 °20.15970629244 °2-0.264042713503 °20.0681717530977 °2---0.233417418023 °2
S0.0258798603246 Å °-0.031269661099 Å °0.00601602852387 Å °-0.111139223502 Å °-0.160528492185 Å °0.082266351334 Å °-0.0299861146124 Å °0.0429710393775 Å °-0.0022242663072 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