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- PDB-6wzs: Fusibacterium ulcerans ZTP riboswitch bound to m-1-pyridinyl AICA -

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Basic information

Entry
Database: PDB / ID: 6wzs
TitleFusibacterium ulcerans ZTP riboswitch bound to m-1-pyridinyl AICA
ComponentsFusibacterium ulcerans ZTP riboswitch
KeywordsRNA / Riboswitch / pseudoknot / Purine Biosynthesis / AICAR
Function / homology: / Chem-UG4 / : / RNA / RNA (> 10)
Function and homology information
Biological speciesFusobacterium ulcerans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.23 Å
AuthorsPichling, P. / Jones, C.P. / Ferre-D'Amare, A.R. / Tran, B.
CitationJournal: Cell Chem Biol / Year: 2020
Title: Parallel Discovery Strategies Provide a Basis for Riboswitch Ligand Design.
Authors: Tran, B. / Pichling, P. / Tenney, L. / Connelly, C.M. / Moon, M.H. / Ferre-D'Amare, A.R. / Schneekloth Jr., J.S. / Jones, C.P.
History
DepositionMay 14, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 24, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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
B: Fusibacterium ulcerans ZTP riboswitch
A: Fusibacterium ulcerans ZTP riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,15216
Polymers48,3952
Non-polymers75714
Water362
1
B: Fusibacterium ulcerans ZTP riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5768
Polymers24,1971
Non-polymers3797
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Fusibacterium ulcerans ZTP riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5768
Polymers24,1971
Non-polymers3797
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.284, 90.284, 121.391
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: RNA chain Fusibacterium ulcerans ZTP riboswitch


Mass: 24197.434 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Fusobacterium ulcerans (bacteria) / References: GenBank: 1370545701
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-UG4 / 5-amino-1-(pyridin-3-yl)-1H-imidazole-4-carboxamide


Mass: 203.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H9N5O / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 2.95 Å3/Da / Density % sol: 58.32 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 26% (w/v) PEG 4000, 100 mM Tris HCl pH 8.5, 200 mM Lithium Sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.98395 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98395 Å / Relative weight: 1
ReflectionResolution: 3.23→50 Å / Num. obs: 9567 / % possible obs: 100 % / Redundancy: 9.4 % / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.03 / Rrim(I) all: 0.093 / Χ2: 0.62 / Net I/σ(I): 3.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.25-3.317.62.5744710.1730.9682.7580.4399.4
3.31-3.378.11.9224740.4630.7092.0520.42100
3.37-3.438.92.1164520.4730.7422.2450.43100
3.43-3.59.91.8244750.5650.6081.9240.444100
3.5-3.58101.4934640.6540.4941.5740.445100
3.58-3.6610.21.2744610.730.421.3430.435100
3.66-3.759.90.8884840.8160.2950.9370.485100
3.75-3.8510.10.7344520.8610.2420.7740.433100
3.85-3.97100.5764890.9120.190.6070.474100
3.97-4.099.70.3914650.9560.1320.4130.441100
4.09-4.249.10.3524720.9640.1230.3730.482100
4.24-4.419.60.2764770.9770.0930.2910.509100
4.41-4.619.50.2234730.9870.0760.2360.547100
4.61-4.8510.10.1584820.9910.0530.1660.638100
4.85-5.16100.1334680.9940.0440.140.713100
5.16-5.569.80.1144870.9960.0380.120.805100
5.56-6.119.10.094950.9950.0320.0960.962100
6.11-79.20.0734860.9970.0250.0771.017100
7-8.819.70.0644960.9980.0220.0671.103100
8.81-508.50.03354410.0120.0351.096100

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.06 Å47.95 Å
Translation6.06 Å47.95 Å

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data scaling
PHASER2.8.3phasing
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5BTP

5btp


Resolution: 3.23→47.95 Å / SU ML: 0.54 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 31.31
RfactorNum. reflection% reflection
Rfree0.2589 948 9.94 %
Rwork0.2239 --
obs0.2274 9537 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 347.79 Å2 / Biso mean: 163.0724 Å2 / Biso min: 74.09 Å2
Refinement stepCycle: final / Resolution: 3.23→47.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2609 42 2 2653
Biso mean--125.02 135.47 -
Num. residues----122
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0012950
X-RAY DIFFRACTIONf_angle_d0.2584584
X-RAY DIFFRACTIONf_dihedral_angle_d13.1511451
X-RAY DIFFRACTIONf_chiral_restr0.014608
X-RAY DIFFRACTIONf_plane_restr0.001128
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.23-3.40.4181320.33641186131899
3.4-3.620.31941310.28712171348100
3.62-3.90.33561340.242611941328100
3.9-4.290.26161380.185712171355100
4.29-4.90.25771310.172412171348100
4.91-6.180.21811380.213712431381100
6.19-47.950.24891440.231613151459100
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)
12.00098.8074-6.70425.7004-3.45295.66272.9047-3.8991-0.36130.6586-1.91481.03841.7456-0.97240.10682.8008-0.6997-1.01573.39880.5941.89318.0312-22.0063-55.0792
23.2470.5909-0.00917.4935-1.16494.82650.77351.1670.8434-0.66790.81840.6221-0.7763-0.4539-0.83841.14490.13480.31381.62920.34030.812426.237-24.4188-38.844
30.7732-1.07481.26553.26890.86495.77630.4621.5644-1.1499-1.207-0.50590.225-1.09-0.044-0.24051.2827-0.1934-0.09172.3995-0.4740.996921.0203-49.3721-43.5672
43.09742.07672.12953.1786-0.07732.6597-0.49481.0178-1.2884-0.61020.8157-0.3731.0906-1.01340.25861.731-0.19420.08291.9236-0.47431.277218.5934-54.9094-43.2518
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 6 through 10 )B6 - 10
2X-RAY DIFFRACTION2chain 'B' and (resid 11 through 75 )B11 - 75
3X-RAY DIFFRACTION3chain 'A' and (resid 6 through 25 )A6 - 25
4X-RAY DIFFRACTION4chain 'A' and (resid 26 through 75 )A26 - 75

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