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- PDB-7rex: PreQ1-1 (type-1) riboswitch in complex with tandem stacked metabolites -

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Basic information

Entry
Database: PDB / ID: 7rex
TitlePreQ1-1 (type-1) riboswitch in complex with tandem stacked metabolites
ComponentsRNA (34-MER)
KeywordsRNA / PREQ1 / PREQ0 / QUEUOSINE / RIBOSOMAL BINDING SITE / APTAMER / METABOLITE / SHINE-DALGARNO SEQUENCE / H-TYPE PSEUDOKNOT / RIBOSWITCH / RNA FOLDING / GENE REGULATION / RNA-LIGAND INTERACTIONS
Function / homology7-DEAZA-7-AMINOMETHYL-GUANINE / RNA / RNA (> 10)
Function and homology information
Biological speciesCarnobacterium antarcticum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsJenkins, J.L. / Schroeder, G.M. / Wedekind, J.E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM63162-14 United States
CitationJournal: Nat Commun / Year: 2022
Title: A small RNA that cooperatively senses two stacked metabolites in one pocket for gene control
Authors: Schroeder, G.M. / Cavender, C.E. / Blau, M.E. / Jenkins, J.L. / Mathews, D.H. / Wedekind, J.E.
History
DepositionJul 13, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 29, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 19, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (34-MER)
B: RNA (34-MER)
C: RNA (34-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,72413
Polymers32,5523
Non-polymers1,17210
Water181
1
A: RNA (34-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2826
Polymers10,8511
Non-polymers4315
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RNA (34-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2093
Polymers10,8511
Non-polymers3582
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: RNA (34-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2334
Polymers10,8511
Non-polymers3833
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.797, 57.797, 153.635
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 22 or (resid 27...
21(chain B and (resid 1 through 22 or (resid 27...
31(chain C and (resid 1 through 33 or resid 36 through 37))

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 1 through 22 or (resid 27...A1 - 22
121(chain A and (resid 1 through 22 or (resid 27...A27
131(chain A and (resid 1 through 22 or (resid 27...A1 - 37
141(chain A and (resid 1 through 22 or (resid 27...A1 - 37
151(chain A and (resid 1 through 22 or (resid 27...A1 - 37
161(chain A and (resid 1 through 22 or (resid 27...A1 - 37
171(chain A and (resid 1 through 22 or (resid 27...A1 - 37
181(chain A and (resid 1 through 22 or (resid 27...A1 - 37
191(chain A and (resid 1 through 22 or (resid 27...A1 - 37
1101(chain A and (resid 1 through 22 or (resid 27...A1 - 37
1111(chain A and (resid 1 through 22 or (resid 27...A1 - 37
1121(chain A and (resid 1 through 22 or (resid 27...A1 - 37
1131(chain A and (resid 1 through 22 or (resid 27...A1 - 37
1141(chain A and (resid 1 through 22 or (resid 27...A1 - 37
1151(chain A and (resid 1 through 22 or (resid 27...A1 - 37
1161(chain A and (resid 1 through 22 or (resid 27...A1 - 37
1171(chain A and (resid 1 through 22 or (resid 27...A1 - 37
1181(chain A and (resid 1 through 22 or (resid 27...A1 - 37
1191(chain A and (resid 1 through 22 or (resid 27...A1 - 37
1201(chain A and (resid 1 through 22 or (resid 27...A1 - 37
211(chain B and (resid 1 through 22 or (resid 27...B1 - 22
221(chain B and (resid 1 through 22 or (resid 27...B27
231(chain B and (resid 1 through 22 or (resid 27...B1 - 33
241(chain B and (resid 1 through 22 or (resid 27...B1 - 33
251(chain B and (resid 1 through 22 or (resid 27...B1 - 33
261(chain B and (resid 1 through 22 or (resid 27...B1 - 33
271(chain B and (resid 1 through 22 or (resid 27...B1 - 33
281(chain B and (resid 1 through 22 or (resid 27...B1 - 33
291(chain B and (resid 1 through 22 or (resid 27...B1 - 33
2101(chain B and (resid 1 through 22 or (resid 27...B1 - 33
2111(chain B and (resid 1 through 22 or (resid 27...B1 - 33
2121(chain B and (resid 1 through 22 or (resid 27...B1 - 33
2131(chain B and (resid 1 through 22 or (resid 27...B1 - 33
2141(chain B and (resid 1 through 22 or (resid 27...B1 - 33
2151(chain B and (resid 1 through 22 or (resid 27...B1 - 33
2161(chain B and (resid 1 through 22 or (resid 27...B1 - 33
2171(chain B and (resid 1 through 22 or (resid 27...B1 - 33
2181(chain B and (resid 1 through 22 or (resid 27...B1 - 33
2191(chain B and (resid 1 through 22 or (resid 27...B1 - 33
311(chain C and (resid 1 through 33 or resid 36 through 37))C1 - 33
321(chain C and (resid 1 through 33 or resid 36 through 37))C36 - 37

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Components

#1: RNA chain RNA (34-MER)


Mass: 10850.541 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Carnobacterium antarcticum (bacteria)
#2: Chemical
ChemComp-PRF / 7-DEAZA-7-AMINOMETHYL-GUANINE


Mass: 179.179 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C7H9N5O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.28 Å3/Da / Density % sol: 45.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.08 M KCl, 0.012 M NaCl, 30% MPD, 0.04 M NaCacodylate pH 5.5, 0.002 M Hexamine Cobalt (III) Chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 9, 2019
Details: Rh coated collimating mirrors, K-B focusing mirrors
RadiationMonochromator: Liquid nitrogen-cooled double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.6→35.8 Å / Num. obs: 17419 / % possible obs: 99.6 % / Redundancy: 4.7 % / CC1/2: 0.994 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.071 / Net I/σ(I): 8.6
Reflection shellResolution: 2.6→2.72 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.88 / Mean I/σ(I) obs: 2 / Num. unique obs: 1382 / CC1/2: 0.863 / Rpim(I) all: 0.677 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
XDSMar 15, 2019data reduction
Aimless0.7.4data scaling
PHASER2.83phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FU2

3fu2


Resolution: 2.6→35.8 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 0.77 / Phase error: 33.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.272 1722 9.89 %
Rwork0.2315 15696 -
obs0.2355 17418 98.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 230.12 Å2 / Biso mean: 91.1092 Å2 / Biso min: 14.78 Å2
Refinement stepCycle: final / Resolution: 2.6→35.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2042 136 1 2179
Biso mean--51.52 18.63 -
Num. residues----97
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A526X-RAY DIFFRACTION10.711TORSIONAL
12B526X-RAY DIFFRACTION10.711TORSIONAL
13C526X-RAY DIFFRACTION10.711TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6-2.680.42831310.42461251138295
2.68-2.760.40951490.41421335148499
2.76-2.860.41811510.3831313146499
2.86-2.980.35451350.33641287142297
2.98-3.110.26291630.25051297146099
3.11-3.280.21511390.17541318145799
3.28-3.480.21521360.2011310144699
3.48-3.750.27671510.21231308145999
3.75-4.130.31391370.21771345148299
4.13-4.720.24651480.200812931441100
4.72-5.920.24771340.21211316145099
5.95-35.80.26061480.22241323147199
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)
14.12130.6571-1.80764.4909-0.47673.19310.09880.0455-0.20460.1332-0.0882-0.19850.27130.2320.03090.49090.1326-0.0550.47630.0380.258724.492623.475146.0867
28.03741.13284.92642.9325-0.87823.9674-0.04221.7673-0.6438-0.8601-0.0483-0.81620.26682.32570.07831.28540.3488-0.12881.6130.18290.605637.670517.02254.8086
32.00183.69381.98352.02462.18122.00760.36291.0753-2.6814-0.71920.5695-0.74391.64510.6358-0.89931.07170.15930.06060.61160.03620.798424.316112.491246.5726
47.89273.61872.49226.08877.69052.00350.1547-0.43910.319-0.0772-0.38111.15230.1487-1.1730.3640.41280.04220.00260.73170.16220.395214.262127.761443.204
58.00261.85447.9832.0136-6.84042.0081.0185-0.0397-0.49570.7612-0.8385-0.09670.99981.3837-0.31930.8906-0.1054-0.15640.60060.1380.423434.20621.449470.9121
64.4166-1.00252.07536.4768-1.08995.33260.2062-0.0673-0.21880.0925-0.09680.1079-0.40320.9346-0.18960.8645-0.1997-0.05590.5850.01890.295134.50419.583682.5808
76.3950.27120.58497.66661.18063.73460.03470.65480.0629-0.5212-0.38770.15790.28610.08280.28560.979-0.1732-0.09080.470.04830.276732.06111.369969.4656
86.18492.8691.98922.01362.39042.01010.4257-0.39481.40681.47530.59620.8569-2.91770.2494-0.98761.4814-0.11360.0270.56620.08630.642427.900827.390568.8015
92.0024-0.1011-5.16165.6053-1.3828.33521.0049-0.45610.41951.32470.05961.2433-0.4202-0.1084-0.80340.733-0.2396-0.13420.7023-0.13530.528722.809114.118876.9096
101.97290.0818-5.38812.00327.24512.0056-0.07060.9973-0.49940.6912-0.5203-0.28281.45620.18160.2541.5511-0.1225-0.38970.5578-0.01360.284534.52351.849677.5364
112.35680.63770.37421.7461-2.01072.00240.46840.0279-0.60480.11880.14080.19111.8894-0.1175-0.4111.4953-0.70950.26032.36190.42960.2427-1.156-3.014567.1443
126.27933.1231-3.97411.7843-1.49313.54860.24480.32550.9026-0.17190.43660.4222-1.2598-0.9774-0.72162.03690.84480.94871.72210.82751.74112.125212.336353.566
134.8376-1.5565-0.00293.9831-0.74750.92650.70730.81780.8288-0.21030.56010.6091-1.0594-1.3038-1.38630.83710.15840.27091.03240.19540.6196.94113.896562.7352
142.3553-1.6957-0.31521.88941.40222.119-0.31421.06130.1425-0.149-0.47070.70640.0038-1.29180.43721.11190.63890.52973.00290.65171.0644-6.75567.176667.0966
154.7306-4.9124.45492.0127-0.68656.24380.16580.19141.851.61090.77940.8841-2.9074-0.524-0.96151.64690.10750.70890.77250.23711.274911.028511.03159.8128
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 20 )A1 - 20
2X-RAY DIFFRACTION2chain 'A' and (resid 21 through 25 )A21 - 25
3X-RAY DIFFRACTION3chain 'A' and (resid 26 through 30 )A26 - 30
4X-RAY DIFFRACTION4chain 'A' and (resid 31 through 34 )A31 - 34
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 5 )B1 - 5
6X-RAY DIFFRACTION6chain 'B' and (resid 6 through 15 )B6 - 15
7X-RAY DIFFRACTION7chain 'B' and (resid 16 through 20 )B16 - 20
8X-RAY DIFFRACTION8chain 'B' and (resid 21 through 25 )B21 - 25
9X-RAY DIFFRACTION9chain 'B' and (resid 26 through 30 )B26 - 30
10X-RAY DIFFRACTION10chain 'B' and (resid 31 through 33 )B31 - 33
11X-RAY DIFFRACTION11chain 'C' and (resid 1 through 5 )C1 - 5
12X-RAY DIFFRACTION12chain 'C' and (resid 6 through 10 )C6 - 10
13X-RAY DIFFRACTION13chain 'C' and (resid 11 through 20 )C11 - 20
14X-RAY DIFFRACTION14chain 'C' and (resid 21 through 29 )C21 - 29
15X-RAY DIFFRACTION15chain 'C' and (resid 30 through 34 )C30 - 34

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