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- PDB-8f4o: Apo structure of the TPP riboswitch aptamer domain -

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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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)

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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

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Experimental details

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Experiment

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

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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

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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

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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

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