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- PDB-6wzr: Fusibacterium ulcerans ZTP riboswitch bound to p-1-pyridinyl AICA -

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Basic information

Entry
Database: PDB / ID: 6wzr
TitleFusibacterium ulcerans ZTP riboswitch bound to p-1-pyridinyl AICA
ComponentsFusibacterium ulcerans ZTP riboswitch
KeywordsRNA / Riboswitch / pseudoknot / Purine Biosynthesis / AICAR
Function / homology: / Chem-UG1 / : / RNA / RNA (> 10)
Function and homology information
Biological speciesFusobacterium ulcerans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.2 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
A: Fusibacterium ulcerans ZTP riboswitch
B: Fusibacterium ulcerans ZTP riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,04511
Polymers48,3952
Non-polymers6519
Water362
1
A: Fusibacterium ulcerans ZTP riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5817
Polymers24,1971
Non-polymers3846
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Fusibacterium ulcerans ZTP riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4644
Polymers24,1971
Non-polymers2673
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.991, 89.991, 122.834
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-102-

K

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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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-UG1 / 5-amino-1-(pyridin-4-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


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: 2.97 Å3/Da / Density % sol: 58.54 %
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, 180 mM Lithium Sulfate, 4% (v/v) PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 9937 / % possible obs: 100 % / Redundancy: 9.6 % / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.029 / Rrim(I) all: 0.088 / Χ2: 0.813 / Net I/σ(I): 5.8 / Num. measured all: 95653
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2
3.2-3.269.51.5034870.60.5111.5880.434
3.26-3.319.21.2174920.6260.4231.290.43
3.31-3.389.90.9464710.8250.3160.9990.436
3.38-3.45100.8664910.8620.2850.9120.461
3.45-3.529.90.7534790.8810.2490.7930.455
3.52-3.69.50.6594980.9130.2240.6960.461
3.6-3.699.80.474850.9380.1570.4950.493
3.69-3.7910.20.394850.9630.1270.410.51
3.79-3.9110.10.3075100.970.1010.3240.548
3.91-4.03100.2424670.980.080.2550.568
4.03-4.189.70.1864960.9870.0630.1970.642
4.18-4.349.20.1574960.9890.0550.1660.761
4.34-4.549.90.144900.9920.0470.1480.768
4.54-4.789.50.1084940.9950.0370.1140.885
4.78-5.089.70.0875070.9970.030.0921.038
5.08-5.47100.0814830.9970.0270.0851.165
5.47-6.029.40.0725140.9960.0250.0761.363
6.02-6.899.30.0655110.9980.0220.0691.48
6.89-8.679.30.0575180.9980.020.0611.545
8.67-508.50.04256310.0160.0451.797

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Phasing

PhasingMethod: molecular replacement

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Processing

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

5btp


Resolution: 3.2→48.24 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 26.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2487 991 10 %
Rwork0.206 8919 -
obs0.2103 9910 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 482.65 Å2 / Biso mean: 151.3555 Å2 / Biso min: 58.18 Å2
Refinement stepCycle: final / Resolution: 3.2→48.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2583 37 2 2622
Biso mean--127.53 115.79 -
Num. residues----121
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0012922
X-RAY DIFFRACTIONf_angle_d0.3174543
X-RAY DIFFRACTIONf_dihedral_angle_d12.1861441
X-RAY DIFFRACTIONf_chiral_restr0.016602
X-RAY DIFFRACTIONf_plane_restr0.002127
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
3.2-3.370.32421390.289212381377
3.37-3.580.29461410.243712521393
3.58-3.850.27471410.197812471388
3.86-4.240.22771430.175512651408
4.24-4.850.2241390.177412641403
4.86-6.110.21471400.192112951435
6.12-48.240.25991480.21713581506
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)
14.67525.0862-5.28175.3511-5.29375.96091.46280.20351.1380.8920.28230.1936-2.1810.7425-1.73711.6226-0.36170.44321.6941-0.35941.3208-26.9173-3.5777-12.9072
23.2458-0.26390.26175.82520.89811.57770.05350.64350.0164-0.46120.7828-0.91240.2990.3163-0.2530.7417-0.16350.02170.8483-0.15880.7501-37.478-10.88120.5892
36.29731.5019-0.47516.3507-2.89546.1191-0.12791.1170.0334-1.27991.4959-2.2444-0.30832.45840.25231.2354-0.27450.2641.6432-0.73451.3482-25.2759-6.99174.0386
48.3536-6.8489-5.17436.37024.01986.1176-0.78662.1936-2.92184.79140.7554-0.1688.9513-0.37380.62934.7562-1.2275-0.60222.79690.07961.7445-60.1609-2.0144-19.1099
56.288-2.23862.85964.1427-2.11349.9667-0.77480.92751.2495-0.107-0.06430.29-0.96020.69490.77221.3681-0.2957-0.1520.87650.2741.1204-49.382910.32193.2133
66.09672.61281.15265.49946.24417.77750.42-3.1568-3.16075.4339-0.99260.16150.5850.040.8272.6846-0.35520.19481.51290.2571.4388-42.968522.90936.2412
75.7386-0.85054.54360.2308-0.82593.61470.5045-2.41563.7821.55831.06541.7942-3.1954-3.6595-1.12752.66730.11230.5931.8633-0.07911.8582-52.391424.456.5149
87.86632.7160.27933.60171.64830.2648-0.0080.7240.6059-1.3160.19510.682-1.2735-0.9101-0.04451.9484-0.0882-0.56941.64340.29361.3811-57.71358.0665-9.071
92.76343.2206-0.09595.79753.16774.7749-0.54530.65630.8453-1.73730.13113.1158-1.4374-2.32150.44711.60470.0122-0.13571.4240.16461.7368-60.516411.47854.7269
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 15 )A6 - 15
2X-RAY DIFFRACTION2chain 'A' and (resid 16 through 50 )A16 - 50
3X-RAY DIFFRACTION3chain 'A' and (resid 51 through 75 )A51 - 75
4X-RAY DIFFRACTION4chain 'B' and (resid 7 through 11 )B7 - 11
5X-RAY DIFFRACTION5chain 'B' and (resid 12 through 26 )B12 - 26
6X-RAY DIFFRACTION6chain 'B' and (resid 27 through 31 )B27 - 31
7X-RAY DIFFRACTION7chain 'B' and (resid 32 through 36 )B32 - 36
8X-RAY DIFFRACTION8chain 'B' and (resid 37 through 63 )B37 - 63
9X-RAY DIFFRACTION9chain 'B' and (resid 64 through 75 )B64 - 75

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