[English] 日本語
Yorodumi
- PDB-8f4o: Apo structure of the TPP riboswitch aptamer domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8f4o
TitleApo structure of the TPP riboswitch aptamer domain
ComponentsTPP riboswitch aptamer domain
KeywordsRNA / Riboswitch / Aptamer / Thiamine pyrophosphate / TPP
Function / homologyIRIDIUM HEXAMMINE ION / TRIETHYLENE GLYCOL / : / RNA / RNA (> 10)
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.1 Å
AuthorsLee, H.-K. / Wang, Y.-X. / Stagno, J.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: Structure / Year: 2023
Title: Crystal structure of Escherichia coli thiamine pyrophosphate-sensing riboswitch in the apo state.
Authors: Lee, H.K. / Lee, Y.T. / Fan, L. / Wilt, H.M. / Conrad, C.E. / Yu, P. / Zhang, J. / Shi, G. / Ji, X. / Wang, Y.X. / Stagno, J.R.
History
DepositionNov 11, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 17, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 21, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 19, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 25, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TPP riboswitch aptamer domain
B: TPP riboswitch aptamer domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,33633
Polymers53,5982
Non-polymers8,73831
Water00
1
A: TPP riboswitch aptamer domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,95419
Polymers26,7991
Non-polymers5,15518
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: TPP riboswitch aptamer domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,38214
Polymers26,7991
Non-polymers3,58313
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)139.264, 139.264, 97.905
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)

-
Components

#1: RNA chain TPP riboswitch aptamer domain


Mass: 26798.936 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli) / References: GenBank: 1845826323
#2: Chemical...
ChemComp-IRI / IRIDIUM HEXAMMINE ION


Mass: 294.400 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: H18IrN6
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.56 Å3/Da / Density % sol: 51.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.1 M Tris-Bicine, pH 8.3, 12.5% MPD, 12.5% PEG 3350, 12.5% PEG 1000, 0.12 M ethylene glycol mixture

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.103025 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 7, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.103025 Å / Relative weight: 1
ReflectionResolution: 3.1→48.95 Å / Num. obs: 19251 / % possible obs: 99.9 % / Redundancy: 14.9 % / Biso Wilson estimate: 142.18 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.041 / Rrim(I) all: 0.122 / Χ2: 1 / Net I/σ(I): 17.6
Reflection shellResolution: 3.1→3.31 Å / % possible obs: 99.8 % / Redundancy: 8.2 % / Rmerge(I) obs: 2.868 / Num. measured all: 15240 / Num. unique obs: 1863 / CC1/2: 0.502 / Rpim(I) all: 1.073 / Rrim(I) all: 3.07 / Χ2: 0.98 / Net I/σ(I) obs: 0.9

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487+SVNrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: SAD
Starting model: 4NYG

4nyg


Resolution: 3.1→45.58 Å / SU ML: 0.4915 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 40.3155
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3166 960 5.15 %
Rwork0.2818 17692 -
obs0.2836 18652 96.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 143.14 Å2
Refinement stepCycle: LAST / Resolution: 3.1→45.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2922 229 0 3151
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00353550
X-RAY DIFFRACTIONf_angle_d1.04955702
X-RAY DIFFRACTIONf_chiral_restr0.0905692
X-RAY DIFFRACTIONf_plane_restr0.0041137
X-RAY DIFFRACTIONf_dihedral_angle_d21.14691670
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.260.35261020.36482071X-RAY DIFFRACTION79.25
3.26-3.470.37761480.34622587X-RAY DIFFRACTION99.09
3.47-3.740.36121340.29592600X-RAY DIFFRACTION99.78
3.74-4.110.28321400.28652605X-RAY DIFFRACTION99.85
4.11-4.710.3181530.28462607X-RAY DIFFRACTION99.89
4.71-5.920.27441140.2642625X-RAY DIFFRACTION99.89
5.93-45.580.32681690.27622597X-RAY DIFFRACTION99.78
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)
10.253229671195-0.364262675143-0.150400875281.97066713158-1.460002338332.14808922312-0.4561017884340.0148800410517-0.556958197551-0.117189749879-0.199579230469-1.135342837460.4587803392360.315276696229-1.818797629511.3141373342-0.100838174230.3190971242740.484376114436-0.3016206703381.14576094109-46.155900985815.2053526416-8.01601099488
20.369596211436-0.4178775293320.08881911175490.6810514235750.4393808107891.496311817290.211726545406-0.04636442282930.223634504584-0.1259300916640.172213920535-0.0135189697206-0.479313721189-0.04366564158630.2865194807370.979623743887-0.342389279788-0.4128137775581.372501326490.8311567429971.92469779193-26.1549338833.85624806195.59279167079
30.0434726227610.3046504300870.3741231989421.994061725992.352030003852.75391452534-0.542218019878-0.0317529775799-0.0760380780880.355876559747-0.5599447139310.126282749141-0.2699537199040.153623085787-0.6647247123340.8713771571470.1141196370250.002946518256560.5943939138080.2951580769651.02767336822-35.552722244228.57104991583.32619284471
41.458899573630.613153556506-0.1502943043122.37611226646-0.2113840457850.0373799307894-0.8463576128170.546373113714-1.05417780553-0.06165679831280.477278886023-0.649610513256-0.171010454804-0.147819647405-1.082321843981.07940784267-0.1368350511660.279037878966-0.0233252193302-0.998606715170.967890439436-44.895060271618.4290206131-3.29406244431
50.348689802905-0.4717007244980.1613234069150.592287685775-0.2089866352910.05847360265490.3251561406450.878103135062-0.440410257463-0.512916204385-0.2262310645080.02197598181750.0487527997613-0.2635089362242.585983377650.8279371057630.6495619477450.2546527944231.37666379515-0.1929477105280.64644640899-47.944914113430.8521119928-19.9258947621
60.2646022475070.873778544722-0.3971595737612.77810719499-0.8774133760270.6523390740420.6928480076910.3500430011780.1135152480690.168960653533-1.210109159320.200785208628-0.530179686947-0.16290587133-0.1364398752880.5555738440280.193213529955-0.04085549956211.627750995990.1348274889790.441465695776-56.813659695554.6984061758-19.8689193717
70.4393312369270.295803034795-0.3204242359240.3219306408490.02428990514750.722576355713-0.0419223748212-0.00286872198533-0.0872690933301-0.371387206816-0.5193787638250.2046227111250.0629470326882-0.124996485001-1.052001500081.665545410150.2228769573590.2785692808352.78967109877-0.9057366398221.4491187163-51.882778432222.8133767454-23.9568334648
80.00964528301423-0.01116337232130.01749764980680.0282345993785-0.0521784290910.0629858002646-0.211368076376-0.0254263800746-0.1222746385410.2938107997190.395867979457-0.704867654442-0.2956764019820.1538421643095.83602517633E-54.160215398990.3138412553810.1061954943412.13205615603-0.114558224461.44419280048-63.19455428653.11204097562-9.13657555954
90.4541924883250.05130002786370.02469902737681.330377324410.3854128412940.1087517609620.02934702463990.3149461245-0.701193528859-0.5700219338120.575098842775-1.181650193520.09341825798850.4757445278370.0456001842422.69107101708-0.655517334359-0.1919187024432.572886433530.3916715773231.57929967815-21.70319259956.1055665769-22.7453916261
100.661677446224-0.156566799992-0.618467960750.03310771246810.1638449881110.560025753643-0.7438808487760.339575387472-0.4541329519940.49085447770.180476359564-0.93481552092-0.362633015171-0.324515877717-0.1084385340540.8586589210340.0139951877782-0.366307238711.042214707520.06992755954711.09796668604-24.064523880341.1732487799-14.3752516905
110.105759704334-0.02125977682570.04891143029780.00389293774694-0.00593321905030.01856291721540.02198235418790.637793438958-0.174197983556-0.311057514241-0.0206693897871-0.2361172055720.03173738144130.3195199656030.1695645521391.689359447530.2545084754050.5391140528781.5927015515-0.2082945867040.764078970628-27.009823513421.9914552618-31.4104087266
120.159624366968-0.00381581644983-0.241140605510.0220680039023-0.0208056158380.334802890759-0.7989364432510.875953261820.2107441100130.28245917421-0.5986851498840.402557731763-0.1680209286980.500006216115-0.03754736380410.774116755996-0.119488396846-0.2337833925191.54502996260.1328536490791.1281796765-25.714955520939.217640879-22.4338919585
130.230832562202-0.2036473199630.1889220006410.909504545447-0.3170935973160.192910973529-0.669931871587-0.3041127973350.5778504506510.709752003246-0.0108196479947-0.3334216043790.0402182752007-0.186224001255-0.05588671979110.7084365937-0.08758786261120.04766247720130.943030301027-0.09866800483831.02122547402-44.555194074740.6264482918-17.692735573
140.07955865007620.0622060659610.02978903489920.0984372958725-0.03647737013790.0628262710163-0.2545708886610.206169285498-0.429556343072-0.7870455150.0388249379536-0.625511116943-0.159155918689-0.802797805427-0.001023526277571.341463686250.289671784381-0.1971129044381.9664962073-0.5792689610621.28565188921-64.971997601438.8929855988-32.9344620001
152.77185083631-1.738127835391.134063377832.949299972620.5277073325965.3077139099-0.3711627302380.209675264770.7221454446090.20217826666-0.549416604038-0.38024927318-0.870554657381-1.06604416556-1.725153039290.832295136820.236962427893-0.2260384782930.8491226175370.1019150201620.554119877948-48.995111428945.0428902999-14.5013573789
161.7533241974-2.05273098702-1.410934900652.392849241671.654278939261.14636237553-0.4295990719360.0243724233752-0.3766513757740.7167121937670.2930539171520.4083058768740.7659421614020.535568243225-0.6627345748451.33721360843-0.0917250076528-0.4932178695770.9871645270070.1087278098940.851733169318-20.714350318756.5420870943-14.0028768597
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 12:21)AA12 - 21
2X-RAY DIFFRACTION2(chain A and resid 22:27)AA22 - 27
3X-RAY DIFFRACTION3(chain A and resid 32:41)AA32 - 41
4X-RAY DIFFRACTION4(chain A and resid 42:51)AA42 - 51
5X-RAY DIFFRACTION5(chain A and resid 52:63)AA52 - 63
6X-RAY DIFFRACTION6(chain A and resid 64:79)AA64 - 79
7X-RAY DIFFRACTION7(chain A and resid 80:84)AA80 - 84
8X-RAY DIFFRACTION8(chain A and resid 85:90)AA85 - 90
9X-RAY DIFFRACTION9(chain B and resid 9:13)BB9 - 13
10X-RAY DIFFRACTION10(chain B and resid 14:20)BB14 - 20
11X-RAY DIFFRACTION11(chain B and resid 21:39)BB21 - 39
12X-RAY DIFFRACTION12(chain B and resid 40:52)BB40 - 52
13X-RAY DIFFRACTION13(chain B and resid 53:64)BB53 - 64
14X-RAY DIFFRACTION14(chain B and resid 65:76)BB65 - 76
15X-RAY DIFFRACTION15(chain B and resid 77:83)BB77 - 83
16X-RAY DIFFRACTION16(chain B and resid 84:89)BB84 - 89

+
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://pdbjlvh1.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