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- PDB-7eag: Crystal structure of the RAGATH-18 k-turn -

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Basic information

Entry
Database: PDB / ID: 7eag
TitleCrystal structure of the RAGATH-18 k-turn
ComponentsRNA (5'-R(*GP*UP*CP*UP*AP*UP*GP*AP*AP*GP*GP*CP*UP*GP*GP*AP*GP*AP*C)-3')
KeywordsRNA / motif / kink-turn
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesClostridium perfringens SM101 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: RNA (5'-R(*GP*UP*CP*UP*AP*UP*GP*AP*AP*GP*GP*CP*UP*GP*GP*AP*GP*AP*C)-3')
D: RNA (5'-R(*GP*UP*CP*UP*AP*UP*GP*AP*AP*GP*GP*CP*UP*GP*GP*AP*GP*AP*C)-3')
A: RNA (5'-R(*GP*UP*CP*UP*AP*UP*GP*AP*AP*GP*GP*CP*UP*GP*GP*AP*GP*AP*C)-3')
B: RNA (5'-R(*GP*UP*CP*UP*AP*UP*GP*AP*AP*GP*GP*CP*UP*GP*GP*AP*GP*AP*C)-3')
E: RNA (5'-R(*GP*UP*CP*UP*AP*UP*GP*AP*AP*GP*GP*CP*UP*GP*GP*AP*GP*AP*C)-3')
F: RNA (5'-R(*GP*UP*CP*UP*AP*UP*GP*AP*AP*GP*GP*CP*UP*GP*GP*AP*GP*AP*C)-3')


Theoretical massNumber of molelcules
Total (without water)36,9466
Polymers36,9466
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.769, 74.908, 136.595
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "C"
d_2ens_1chain "D"
d_3ens_1chain "E"
d_4ens_1chain "F"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-ID
d_11ens_1GCA
d_21ens_1GCB
d_31ens_1GCE
d_41ens_1GCF

NCS oper:
IDCodeMatrixVector
1given(-0.999959826119, 0.00110777170262, -0.00889488559551), (-0.00885587314596, -0.275481920786, 0.961265460126), (-0.00138551749359, 0.96130561434, 0.275480663894)31.8817749134, 0.075637973885, 0.0491836623137
2given(-0.00602047805206, -0.30272940873, -0.953057531807), (-0.00491105511014, -0.953054359683, 0.302759424341), (-0.999969817235, 0.00650327453114, 0.00425112204516)31.3932336651, -0.0649367647362, 52.1631514395
3given(0.0124307368756, -0.824553273741, -0.565647748642), (0.0205876090716, 0.565782592849, -0.824297402629), (0.99971077174, -0.00139871060194, 0.0240086749989)31.036696196, -0.704533957017, 19.6566756183

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Components

#1: RNA chain
RNA (5'-R(*GP*UP*CP*UP*AP*UP*GP*AP*AP*GP*GP*CP*UP*GP*GP*AP*GP*AP*C)-3')


Mass: 6157.722 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) Clostridium perfringens SM101 (bacteria)

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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: 2.17 Å3/Da / Density % sol: 43.39 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.2 M Ammonium Acetate, 0.1 M tri-Sodium Citrate dihydrate pH 5.6, 30 % v/v 2-Methyl-2,4-pentanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9119 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 2, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9119 Å / Relative weight: 1
ReflectionResolution: 2.4→65.68 Å / Num. obs: 12955 / % possible obs: 99.87 % / Observed criterion σ(I): 0.3 / Redundancy: 6.3 % / Biso Wilson estimate: 90.11 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.019 / Net I/σ(I): 20.2
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 6.4 % / Rmerge(I) obs: 1.5 / Num. unique obs: 637 / CC1/2: 0.666 / Rpim(I) all: 0.717 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4CS1

4cs1


Resolution: 2.5→65.68 Å / SU ML: 0.4302 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.0669
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2746 534 4.67 %
Rwork0.2177 10893 -
obs0.2202 11427 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 120.91 Å2
Refinement stepCycle: LAST / Resolution: 2.5→65.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2040 0 0 2040
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00252284
X-RAY DIFFRACTIONf_angle_d0.59133556
X-RAY DIFFRACTIONf_chiral_restr0.0321470
X-RAY DIFFRACTIONf_plane_restr0.00695
X-RAY DIFFRACTIONf_dihedral_angle_d14.8971117
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.411143050882
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.992609614896
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS1.06059745828
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.750.37521470.37592642X-RAY DIFFRACTION99.43
2.75-3.150.40591250.3442698X-RAY DIFFRACTION99.02
3.15-3.970.29061230.25942724X-RAY DIFFRACTION99.37
3.97-65.680.24271390.16932829X-RAY DIFFRACTION99.4
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)
15.252204180620.2419088668550.6754201427397.31127386131-5.654974764924.64219667401-0.0809371876414-0.1354590958320.6116357914560.445093400976-0.232134218182-0.5861428574520.560781578736-0.4701713359870.125005934771.14214292788-0.0795809554972-0.07815580125620.486249441234-0.07768393674291.062711341223.781257568512.29664653316.8322874035
26.630139878352.390021974235.209676825637.49107466966-0.369062630586.920888234650.305753695328-2.041018024061.057476411790.978141393278-0.3722767190070.2791673633-0.795730227401-0.134849445299-0.03712479798751.15852863566-0.15987830854-0.03380577593651.52164099792-0.1474421108550.6635403288928.148586479659.7319065475317.4937932729
35.76675193871-0.645611031871.231564522069.825057906053.103859133732.04810917369-0.025771215806-0.0524941894794-0.11988197785-0.953703839291-0.448982587662-0.308176931543-0.4725017521581.028131657960.5327232682771.2360795655-0.0690528607922-0.03367840085971.339408797170.2049767619130.5958602896377.65323561162-1.345803798189.92462151637
46.22719190305-1.342321165290.188629235084.85451604319-5.641751088256.625900966450.838869125234-2.57182435929-0.1131543156391.33955017394-0.334827808061-0.6242304248090.0860584059438-0.33553948421-0.5976971536041.23752750273-0.310552439378-0.1496492176311.69943507790.02076607494920.5066683993768.525779275447.2294154784717.2520199891
56.53986949699-4.440074925874.058324361936.66405745778-2.555986908685.92357952664-0.710402772225-3.703980140881.870022999372.30152164040.907017622268-0.00393286201902-0.701378341755-1.406678414240.6163582726551.25614376737-0.11279568339-0.1524512709040.9597233582-0.7552446084961.807516661419.925924241219.235233140317.904823342
65.560702316754.123476452.696082591924.513800763825.349355455978.794575971170.0947800455256-0.16365894124-0.2960053218960.584834797133-0.591277910572-0.1168399967612.040876790221.30379554140.2802697185991.428136038340.108900216406-0.1699295414770.6253374756520.05986218677841.3311000865428.06984953527.54416566549.51509149177
74.152839140973.678318070531.111208566574.274636430483.293671439034.43473395410.2992639891380.504500029375-0.294356386251-0.3844198546880.00470529364422-0.100947728215-0.461725640197-0.315751567167-0.4960114014780.8101934423730.0198424441831-0.04546885765640.742000208172-0.041581929450.8464788688314.220717039430.0268931599-4.75472421153
85.966417654141.46756940721-0.1860954272478.34085700959-1.279605288445.78226614325-0.1193461887280.0801176080042-2.12864550622-0.4011909852020.039077535349-0.1339596727380.709328392088-0.5902217794810.1287149271550.880825349149-0.0570169945856-0.1086537085390.6238366033-0.02072058211691.0593091240219.476242637428.0540369201-2.69659040587
96.910153896595.54321634012-2.334937522834.5021906192-2.331469309397.67702711783-0.142776235688-0.72469840949-3.303777539231.022492299690.574075919904-2.455480362940.575242351493-0.103609694395-0.5327592180791.375002649820.0994103199844-0.1973766946951.040004093940.227823592851.7616997036926.8146008477-8.9943058005128.7485609002
102.335648949352.44188031874-3.304787919577.08985002373-1.899666583959.22905657739-0.289153915338-1.37900087088-1.896908906130.3719576339890.386643650343-0.9753413619910.776476766258-0.8543071749240.4939932639321.21402501313-0.227773928332-0.1368165857551.498875226740.5343121428041.4568682845515.6309885539-10.499916452429.342002004
113.861190492833.63584179774-1.781305709275.0705279552-0.4391319097363.7993973721-0.166112490666-0.561329530129-0.343249671950.96374875374-0.3337629706691.60652036889-0.940878272598-0.265739153809-0.16096049191.834295958350.05197399934270.2577337697142.198982696650.5347743527681.064345171435.16860037765-4.4213292127540.7910046267
123.933715344273.048720826281.052972990917.15167627876-2.866574160357.689006741561.34393553527-1.83708059437-0.05190470914581.250937965610.004226835603860.4545220312540.425079573122-1.39243400233-0.8909945408412.250280977170.407971517443-0.2557671056381.921349505780.3371041314551.0416071648420.0747957949-3.8173094630247.0320389432
135.786076567115.2982450901-5.794509189854.9854981248-4.897312681616.545186335080.5012027341260.119670138354.13834161872-0.269836132510.2427436545891.014622116760.422643799522-0.867506944549-0.501425575451.781760075720.3572421370510.1307105865711.855913396810.1377671668521.3988051089522.34736155764.1305981088742.9958216
147.873792042142.08136416687-0.1290072470185.807325475013.803361943862.809715693910.342481269905-1.677833060880.97377480557-0.4715410914830.549804043731.08811146131.844107031480.122671380718-0.9348383739571.909672959920.355911126060.09191569510882.032364867290.5900459578331.1101172839712.602654604-2.0921382333642.9924117267
157.02989489516-1.96907717735-2.276436081120.5356615018670.2190196946018.20202032751-0.479668083392-0.720869045183-3.116816733331.155613841580.5461457403510.9313173235222.33760416395-2.08979849232-0.2802429385872.03392599714-0.465882660164-0.08732077722461.941729720250.6141056982241.052263720347.95776748443-13.033274481731.9124245502
164.278617943916.150971848121.891321007078.987284768794.291105506468.730301222050.2504921370432.133594372580.4219345565540.1270926928430.8382268266591.454692266442.07470550239-0.559372676504-0.8768641801621.580213516450.04017527651720.1055294087611.452120722650.2431975598571.2692617290119.9494394946-4.3900224065624.9389568361
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'C' and (resid 1 through 10 )CA1 - 10
2X-RAY DIFFRACTION2chain 'C' and (resid 11 through 19 )CA11 - 19
3X-RAY DIFFRACTION3chain 'D' and (resid 1 through 5 )DB1 - 5
4X-RAY DIFFRACTION4chain 'D' and (resid 6 through 10 )DB6 - 10
5X-RAY DIFFRACTION5chain 'D' and (resid 11 through 15 )DB11 - 15
6X-RAY DIFFRACTION6chain 'D' and (resid 16 through 19 )DB16 - 19
7X-RAY DIFFRACTION7chain 'A' and (resid 1 through 11 )AC1 - 11
8X-RAY DIFFRACTION8chain 'B' and (resid 12 through 19 )BD12 - 19
9X-RAY DIFFRACTION9chain 'E' and (resid 1 through 5 )EE1 - 5
10X-RAY DIFFRACTION10chain 'E' and (resid 6 through 10 )EE6 - 10
11X-RAY DIFFRACTION11chain 'E' and (resid 11 through 15 )EE11 - 15
12X-RAY DIFFRACTION12chain 'E' and (resid 16 through 19 )EE16 - 19
13X-RAY DIFFRACTION13chain 'F' and (resid 1 through 5 )FF1 - 5
14X-RAY DIFFRACTION14chain 'F' and (resid 6 through 10 )FF6 - 10
15X-RAY DIFFRACTION15chain 'F' and (resid 11 through 15 )FF11 - 15
16X-RAY DIFFRACTION16chain 'F' and (resid 16 through 19 )FF16 - 19

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