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- PDB-8vpv: Class III PreQ1 riboswitch mutant delta84 -

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Basic information

Entry
Database: PDB / ID: 8vpv
TitleClass III PreQ1 riboswitch mutant delta84
ComponentsRNA (101-MER)
KeywordsRNA / PREQ1 / QUEUOSINE / THREE-WAY HELICAL JUNCTION / APTAMER / METABOLITE / TRANSLATIONAL REGULATION / HL(OUT)-TYPE PSEUDOKNOT / RIBOSWITCH
Function / homology7-DEAZA-7-AMINOMETHYL-GUANINE / : / RNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciesFaecalibacterium prausnitzii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3.04 Å
AuthorsSrivastava, Y. / Jenkins, J.L. / 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: Nucleic Acids Res. / Year: 2024
Title: Two riboswitch classes that share a common ligand-binding fold show major differences in the ability to accommodate mutations.
Authors: Srivastava, Y. / Akinyemi, O. / Rohe, T.C. / Pritchett, E.M. / Baker, C.D. / Sharma, A. / Jenkins, J.L. / Mathews, D.H. / Wedekind, J.E.
History
DepositionJan 17, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (101-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4892
Polymers32,3101
Non-polymers1791
Water181
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.685, 82.685, 282.007
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: RNA chain RNA (101-MER)


Mass: 32310.047 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Faecalibacterium prausnitzii (bacteria) / References: GenBank: 2094528044
#2: Chemical ChemComp-PRF / 7-DEAZA-7-AMINOMETHYL-GUANINE


Mass: 179.179 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H9N5O / Feature type: SUBJECT OF INVESTIGATION
#3: 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
Has protein modificationN

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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: 4.3 Å3/Da / Density % sol: 71.42 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 3.5 M Sodium Malonate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 4, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 3.04→39.29 Å / Num. obs: 11152 / % possible obs: 99.9 % / Redundancy: 9.1 % / CC1/2: 0.911 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.056 / Rrim(I) all: 0.124 / Χ2: 0.98 / Net I/σ(I): 8.9
Reflection shellResolution: 3.04→3.31 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.662 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1954 / CC1/2: 0.991 / Rpim(I) all: 0.327 / Χ2: 1.01 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
Aimless0.7.4data scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 3.04→39.29 Å / SU ML: 0.53 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 42.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2997 1121 10.07 %
Rwork0.2476 --
obs0.2527 11127 94.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.04→39.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2131 0 1 2132
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0012376
X-RAY DIFFRACTIONf_angle_d0.3333699
X-RAY DIFFRACTIONf_dihedral_angle_d13.5751187
X-RAY DIFFRACTIONf_chiral_restr0.018494
X-RAY DIFFRACTIONf_plane_restr0.001100
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.04-3.180.41271340.44321185X-RAY DIFFRACTION93
3.18-3.350.42971310.38411179X-RAY DIFFRACTION94
3.35-3.560.44311350.40391181X-RAY DIFFRACTION92
3.56-3.830.43551390.35911214X-RAY DIFFRACTION94
3.83-4.220.33281420.29511258X-RAY DIFFRACTION97
4.22-4.830.30571440.26471298X-RAY DIFFRACTION98
4.83-6.070.30811460.26231307X-RAY DIFFRACTION97
6.08-39.290.2411500.18241384X-RAY DIFFRACTION94
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)
13.78570.12121.88213.0321-3.04854.1483-0.39590.786-0.3235-1.60320.7543-0.2266-1.20331.46711.03042.06380.3849-0.17391.262-0.04080.827438.694731.9447112.7623
24.38422.5628-0.54724.2084-3.29557.0461-0.19640.96070.4948-0.14490.36350.5852-0.79380.32940.19241.37390.4547-0.02471.3306-0.07440.749737.032333.313111.995
31.9124-0.0155-0.36498.937-7.00095.5867-0.6543-0.3980.68821.9882.5770.8063-2.3711-3.76298.11632.31470.677-0.09242.6986-0.43420.925328.811933.2027139.9806
43.1352.8045-0.32544.2847-3.98857.75991.13880.57830.38334.12860.6123-1.47931.5497-0.9009-1.08833.10450.43150.01023.83430.03232.171528.694527.9799158.1315
53.0206-2.7979-0.08617.7846-4.37083.81-1.9414-1.91720.8349-0.11920.3391-1.69570.54080.27791.3411.58360.446-0.02911.42010.12561.050932.400727.0478143.6616
60.0450.66870.2038.93472.69830.81710.0976-0.14850.18913.6902-1.1724-0.531.0938-0.77020.06271.99230.5169-0.14762.6987-0.1860.857924.707735.4073128.0716
70.00960.0312-0.07790.1056-0.26950.6532-0.03140.3372-0.1883-0.25370.0680.11040.0733-0.44970.73361.61840.3330.48952.51960.07340.56319.301539.3724106.3297
82.9609-0.08360.57831.51793.05046.3167-0.4974-0.36080.6614-0.9905-0.05390.0318-2.0290.0583-0.46341.41260.0377-0.08071.1205-0.13070.42627.72551.8087109.723
90.67450.0199-0.12440.2734-0.38642.38150.2890.30540.38390.22020.1453-0.2306-1.184-0.24640.41932.92820.19790.1361.582-0.14660.01880.227859.2637101.9735
102.5287-1.1896-1.02412.07311.43074.068-0.36920.192-0.41050.0680.6426-0.11490.42820.20382.15621.98070.44680.25851.8938-0.2658-0.159814.655147.4111.6901
114.69016.7113-3.23229.6159-4.96369.4305-2.9573-2.3882-1.1743-1.9072.8111.58081.9896-1.0819-0.01752.64360.0073-0.72992.04140.71681.658614.077931.9943109.7817
127.5499-0.3296-2.46966.40372.78762.8139-0.2561-0.41431.6153-1.60380.75640.2161-2.6085-0.0852-0.48272.09130.36430.1991.71610.10270.869642.13938.161397.1426
130.4139-0.1782-0.96293.1513-2.21964.1294-0.76640.4161-0.3957-1.4055-0.8129-0.95471.63262.5422-0.15022.4208-0.53140.4243.39950.26810.850663.777425.866893.7691
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 10 )
2X-RAY DIFFRACTION2chain 'A' and (resid 11 through 22 )
3X-RAY DIFFRACTION3chain 'A' and (resid 23 through 30 )
4X-RAY DIFFRACTION4chain 'A' and (resid 31 through 40 )
5X-RAY DIFFRACTION5chain 'A' and (resid 41 through 46 )
6X-RAY DIFFRACTION6chain 'A' and (resid 47 through 51 )
7X-RAY DIFFRACTION7chain 'A' and (resid 52 through 56 )
8X-RAY DIFFRACTION8chain 'A' and (resid 57 through 63 )
9X-RAY DIFFRACTION9chain 'A' and (resid 64 through 72 )
10X-RAY DIFFRACTION10chain 'A' and (resid 73 through 79 )
11X-RAY DIFFRACTION11chain 'A' and (resid 80 through 83 )
12X-RAY DIFFRACTION12chain 'A' and (resid 85 through 94 )
13X-RAY DIFFRACTION13chain 'A' and (resid 95 through 101 )

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