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- PDB-8vvj: Structure of S. odontolytica ZTP riboswitch bound to m-1-pyridiny... -

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Basic information

Entry
Database: PDB / ID: 8vvj
TitleStructure of S. odontolytica ZTP riboswitch bound to m-1-pyridinyl-AICA
ComponentsRNA (64-MER)
KeywordsRNA / riboswitch / drug / synthetic / aptamer
Function / homology: / RNA / RNA (> 10)
Function and homology information
Biological speciesSchaalia odontolytica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsJones, C.P. / Ferre D'Amare, A.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI) United States
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2025
Title: Machine Learning-Augmented Molecular Dynamics Simulations (MD) Reveal Insights Into the Disconnect Between Affinity and Activation of ZTP Riboswitch Ligands.
Authors: Fullenkamp, C.R. / Mehdi, S. / Jones, C.P. / Tenney, L. / Pichling, P. / Prestwood, P.R. / Ferre-D'Amare, A.R. / Tiwary, P. / Schneekloth, J.S.
History
DepositionJan 31, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 11, 2025Provider: repository / Type: Initial release
Revision 1.1Aug 6, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title ..._citation.journal_volume / _citation.title / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (64-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1105
Polymers20,7821
Non-polymers3274
Water1,36976
1
A: RNA (64-MER)
hetero molecules

A: RNA (64-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,21910
Polymers41,5652
Non-polymers6548
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_655-x+1,-y,z1
Buried area6090 Å2
ΔGint-86 kcal/mol
Surface area19320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.247, 118.247, 202.054
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number177
Space group name H-MP622

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Components

#1: RNA chain RNA (64-MER)


Mass: 20782.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schaalia odontolytica (bacteria)
Production host: in vitro transcription vector pT7-TP(deltai) (others)
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-A1AD3 / (1M)-5-amino-1-(1,8-naphthyridin-3-yl)-1H-imidazole-4-carboxamide


Mass: 254.247 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H10N6O / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / 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

Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: 125-300 mM lithium sulfate, 23-27% PEG 3350, 0.1 M Hepes pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 26, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.15→101.03 Å / Num. obs: 85958 / % possible obs: 99.89 % / Redundancy: 39.1 % / CC1/2: 0.997 / Rmerge(I) obs: 0.2546 / Net I/σ(I): 12.41
Reflection shellResolution: 2.15→2.227 Å / Rmerge(I) obs: 2.508 / Num. unique obs: 4513 / CC1/2: 0.831

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→101.03 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 39.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3339 2937 3.42 %
Rwork0.3118 --
obs0.3126 85958 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.15→101.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1376 28 70 1474
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051567
X-RAY DIFFRACTIONf_angle_d0.9182448
X-RAY DIFFRACTIONf_dihedral_angle_d12.233766
X-RAY DIFFRACTIONf_chiral_restr0.039319
X-RAY DIFFRACTIONf_plane_restr0.00767
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.190.47771410.41173963X-RAY DIFFRACTION100
2.19-2.220.32031380.39833931X-RAY DIFFRACTION100
2.22-2.260.38141400.4153927X-RAY DIFFRACTION100
2.26-2.310.39571380.37193983X-RAY DIFFRACTION100
2.31-2.350.35971430.35173956X-RAY DIFFRACTION100
2.35-2.410.36331390.34413977X-RAY DIFFRACTION100
2.41-2.460.41661450.35583957X-RAY DIFFRACTION100
2.46-2.520.41121440.35743947X-RAY DIFFRACTION100
2.52-2.590.40021390.36713923X-RAY DIFFRACTION100
2.59-2.670.38361410.37483943X-RAY DIFFRACTION100
2.67-2.750.43281390.39133989X-RAY DIFFRACTION100
2.75-2.850.46421390.40053936X-RAY DIFFRACTION100
2.85-2.970.32021400.36463961X-RAY DIFFRACTION100
2.97-3.10.35851380.30693943X-RAY DIFFRACTION100
3.1-3.260.30751390.28663954X-RAY DIFFRACTION100
3.26-3.470.30261330.27063942X-RAY DIFFRACTION100
3.47-3.740.28081460.26343935X-RAY DIFFRACTION100
3.74-4.110.3111380.29723955X-RAY DIFFRACTION100
4.11-4.710.35221370.30213966X-RAY DIFFRACTION100
4.71-5.930.27881400.26913964X-RAY DIFFRACTION100
5.93-101.030.28581400.27023969X-RAY DIFFRACTION100
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)
15.7901-3.3329-4.06243.83761.61293.5545-1.3544-0.208-1.5251.04630.5493-0.18440.83590.53670.60670.22150.04670.09860.7126-0.04571.083549.6759-11.414218.6035
20.46530.4925-0.27952.7769-0.41672.435-0.0895-0.0732-0.1812-0.05960.005-0.23990.16940.2158-0.05070.18870.0325-0.00160.2966-0.00440.375231.6836-3.388419.4617
31.8541-1.7439-0.2992.35440.60662.9443-0.12970.0231-0.2493-0.1615-0.05470.69330.1278-0.46050.10450.3029-0.1098-0.00940.45330.00710.551978.8135-4.852111.628
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 10 )
2X-RAY DIFFRACTION2chain 'A' and (resid 11 through 45 )
3X-RAY DIFFRACTION3chain 'A' and (resid 46 through 64 )

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