[English] 日本語
Yorodumi
- PDB-8fza: Class I type III preQ1 riboswitch from E. coli -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8fza
TitleClass I type III preQ1 riboswitch from E. coli
ComponentsPreQ1 Riboswitch (30-MER)
KeywordsRNA / riboswitch / prequeuosine1 / preQ1 / pseudoknot / A-amino kissing / bound state
Function / homology: / 7-DEAZA-7-AMINOMETHYL-GUANINE / : / RNA / RNA (> 10)
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsWedekind, J.E. / Schroeder, G.M. / Jenkins, J.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM063162 United States
CitationJournal: J.Biol.Chem. / Year: 2023
Title: Structure and function analysis of a type III preQ 1 -I riboswitch from Escherichia coli reveals direct metabolite sensing by the Shine-Dalgarno sequence.
Authors: Schroeder, G.M. / Kiliushik, D. / Jenkins, J.L. / Wedekind, J.E.
History
DepositionJan 27, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 30, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PreQ1 Riboswitch (30-MER)
B: PreQ1 Riboswitch (30-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6468
Polymers19,0672
Non-polymers5786
Water55831
1
A: PreQ1 Riboswitch (30-MER)
hetero molecules


  • defined by author
  • Evidence: isothermal titration calorimetry, One equivalent of riboswitch 30-mer binds one equivalent of preQ1 ligand., homology, Other homologous preQ1 riboswitches of class 1 type I and type II form ...Evidence: isothermal titration calorimetry, One equivalent of riboswitch 30-mer binds one equivalent of preQ1 ligand., homology, Other homologous preQ1 riboswitches of class 1 type I and type II form similar tertiary structures. They do not form higher order assemblies in gel filtration.
  • 9.82 kDa, 1 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)9,8234
Polymers9,5341
Non-polymers2893
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PreQ1 Riboswitch (30-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,8234
Polymers9,5341
Non-polymers2893
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.739, 32.272, 51.206
Angle α, β, γ (deg.)90.000, 96.930, 90.000
Int Tables number3
Space group name H-MP121
Space group name HallP2y
Symmetry operation#1: x,y,z
#2: -x,y,-z

-
Components

#1: RNA chain PreQ1 Riboswitch (30-MER)


Mass: 9533.719 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli) / References: GenBank: DADKPC010000024.1
#2: Chemical ChemComp-PRF / 7-DEAZA-7-AMINOMETHYL-GUANINE


Mass: 179.179 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H9N5O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 2.01 Å3/Da / Density % sol: 38.82 % / Description: flat parallel piped
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 31% MPD, 0.05 M Na-cacodylate pH 6.0, 0.012 spermine-HCl, 0.1 M KCl and 0.002 M MgCl2, 0.005 M MnCl2-tetrahydrate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1.85 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 4, 2022
Details: Flat Si Rh coated M0, Kirkpatrick-Baez flat bent Si M1 & M2
RadiationMonochromator: Liquid nitrogen-cooled double crystal Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.85 Å / Relative weight: 1
ReflectionResolution: 2.3→36.53 Å / Num. obs: 12805 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / Redundancy: 22 % / Biso Wilson estimate: 52.92 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.024 / Χ2: 0.94 / Net I/σ(I): 16.7
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 16.3 % / Mean I/σ(I) obs: 2.8 / Num. unique obs: 1388 / CC1/2: 0.917 / Rpim(I) all: 0.271 / Χ2: 0.74 / % possible all: 97.9

-
Processing

Software
NameVersionClassification
Blu-Ice2022data collection
XDSversion 10-Jan-2022data reduction
Aimless0.7.7data scaling
PHENIX1.19.2_4158phasing
Coot0.9.8.5model building
PHENIX1.19.2_4158model building
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: SAD / Resolution: 2.3→36.53 Å / SU ML: 0.3486 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.9496
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2522 1282 10.01 %
Rwork0.2053 11523 -
obs0.2099 12805 97.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 58.31 Å2
Refinement stepCycle: LAST / Resolution: 2.3→36.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1167 30 31 1228
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00161329
X-RAY DIFFRACTIONf_angle_d0.46472062
X-RAY DIFFRACTIONf_chiral_restr0.0227275
X-RAY DIFFRACTIONf_plane_restr0.002659
X-RAY DIFFRACTIONf_dihedral_angle_d13.5876676
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.390.40271400.38161248X-RAY DIFFRACTION96.66
2.39-2.50.40771490.32361325X-RAY DIFFRACTION97.55
2.5-2.630.36691390.30411244X-RAY DIFFRACTION95.71
2.63-2.80.33241410.30391285X-RAY DIFFRACTION98.01
2.8-3.020.35251440.29221290X-RAY DIFFRACTION96.7
3.02-3.320.23831420.20261281X-RAY DIFFRACTION97.07
3.32-3.80.26321410.1741262X-RAY DIFFRACTION95.57
3.8-4.780.21191400.16721295X-RAY DIFFRACTION98.76
4.79-36.530.17451460.16191293X-RAY DIFFRACTION97.96
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)
17.806441354030.4237064530080.2578039611166.70427741071.381946429973.776467407550.2213729019660.5336625074060.487366090834-0.574040179679-0.4366820749420.9180141737730.0917714595129-0.6383085129490.034692495850.5898827316210.0714768178866-0.08371961759590.409682439937-0.01022769668580.628265247549-18.3188074062-17.26376164959.77833349837
28.01494424502-2.257216131531.07949543954.67433097641-1.974599566092.38747414816-0.917976307963-1.595775361590.2454615461541.331689557830.8880475454680.0522617478839-0.110542624387-1.01576565007-0.08891109175710.59780901220.195068337535-0.02684385068290.55501421722-0.01570962736680.384490800051-26.6944717087-5.5956358358716.4164166227
32.900232957661.303267220872.445570126956.87676482952-2.269534023416.32684342117-0.763252969753-1.22191235234-1.147129802330.7346777411760.490602251125-0.2648777925281.024110119110.4760356898290.2894373961140.4127158420250.0905710152398-0.01793565095070.4796814077090.112518485390.453929699998-27.9189667836-8.040609556597.79171829419
41.8470266447-0.6101258109030.9672810767542.51732725008-2.60705965792.6536734810.170367910833-0.725902608231-0.323533106141-0.8662678779241.47993676722-0.06080914408780.244252910915-0.324651452643-1.672921874810.5687990597710.0279713051510.05664627284760.5061159911420.03034162791570.691623639512-17.7584451093-4.905220423256.24107078163
57.401586111090.04892125369760.5848265422092.446306943714.668256218519.08654810311-0.477940702503-0.73488421291-0.2359131689621.3573443521-0.05593512023240.8832075656770.851591185048-0.07387038549730.5545405029050.6253206294040.17842870634-0.003369819584180.490094044844-0.03432897794840.612594431037-12.1367143257-15.978076981215.6611124082
63.38406673738-1.44199490295-0.3167272358363.284622799174.149928784076.11443938657-1.37334964792-1.07260852536-0.1034979523952.324649698060.837951211081.548644414751.3801182565-0.2336661835410.4676228048331.044581141430.4526833017410.1710697712241.210908195860.1723858954460.951857874948-17.9838937028-14.947705402722.7440900849
74.396281800370.914908946549-1.805370887694.29570752874-3.804389616916.63706510147-0.103787992727-0.5443612423711.049808714780.9882886482180.388958867576-0.16432061243-1.033865828040.356402734591-0.3382105849380.5651243456050.123925375659-0.01710742824630.422555602192-0.1264005013450.410575769075-24.27823512040.80720578010411.4468096035
86.4156860085-1.377130890621.010504241172.08206122028-0.2700627131432.045681213060.4348863256880.761163227906-0.350853733308-0.23192925267-0.4109482667780.3963887403830.18965967436-0.1292445255110.01525749600710.5398026274260.1536274849860.05347638226930.438558036006-0.05541763726570.697700445725-0.396655357319.227926619057.8556990833
93.87622839915-0.5190433300153.219996805476.344424817912.72717240184.360841609550.07705336725651.264627216760.930331465429-0.216690314014-0.4398235653151.20667794174-0.6014741025180.3124140765470.4782655888010.4693051053260.1397598081730.005880083174170.5232445409190.05348678447470.5166243601268.314177290551.300262862118.6195018232
100.831406629869-0.2005104458510.7557770726943.051008651661.522332742383.14637337937-0.107212114814-0.690147322878-0.134344754071.174087676260.2371303207761.027133175420.201706869821-0.61356872258-0.1721211010250.5864831355860.3115134578690.1034802173520.5934278369140.3660326685780.963324658261-3.070193348960.45797619129414.6840600113
116.382808214592.30519139092-0.9110786668495.23961394872.273559158477.921890975850.05986522265260.1164508201140.984111510560.514155453605-0.600037108628-0.1606632492220.4767424371111.09586070770.1258101628950.4634587903270.155216016581-0.01072802596560.552227839101-0.04611475762780.592030851923-4.9761170973515.436577706112.4561177239
125.183587397820.0685606207148-0.2873864904595.94878786133-0.3708530505773.73080631624-0.8766169521010.452250483508-0.8509427312980.7695567782510.503929852331-0.373116555046-0.6833038676290.6896792477090.5932526084720.7288061970860.2488431986510.08682382366690.66082690357-0.009612964315871.033586286863.8296643198416.682965140511.283741885
136.233648674870.665845584651-0.3243812217251.66146509197-2.021978718635.84463696618-0.330830971802-1.349370308380.03754841617530.893265343214-0.4331320578180.371508552053-0.155495427068-0.5431475172290.8215378772940.6327753616640.2121950152080.08445757367730.67452646217-0.0197729651510.5299546738387.12164346007-0.25281479081117.9161589942
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 4 )AA1 - 4
2X-RAY DIFFRACTION2chain 'A' and (resid 5 through 8 )AA5 - 8
3X-RAY DIFFRACTION3chain 'A' and (resid 9 through 12 )AA9 - 12
4X-RAY DIFFRACTION4chain 'A' and (resid 13 through 16 )AA13 - 16
5X-RAY DIFFRACTION5chain 'A' and (resid 17 through 20)AA17 - 20
6X-RAY DIFFRACTION6chain 'A' and (resid 21 through 24 )AA21 - 24
7X-RAY DIFFRACTION7chain 'A' and (resid 25 through 30 )AA25 - 30
8X-RAY DIFFRACTION8chain 'B' and (resid 2 through 7)BG2 - 7
9X-RAY DIFFRACTION9chain 'B' and (resid 8 through 11)BG8 - 11
10X-RAY DIFFRACTION10chain 'B' and (resid 12 through 15)BG12 - 15
11X-RAY DIFFRACTION11chain 'B' and (resid 16 through 19)BG16 - 19
12X-RAY DIFFRACTION12chain 'B' and (resid 20 through 26)BG20 - 26
13X-RAY DIFFRACTION13chain 'B' and (resid 27 through 30)BG27 - 30

+
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