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- PDB-3sd3: The structure of the tetrahydrofolate riboswitch containing a U25... -

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Basic information

Entry
Database: PDB / ID: 3sd3
TitleThe structure of the tetrahydrofolate riboswitch containing a U25C mutation
ComponentsTetrahydrofolate riboswitch
KeywordsRNA / tetrahydrofolate rna riboswitch
Function / homologyChem-FFO / IRIDIUM HEXAMMINE ION / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å
AuthorsReyes, F.E. / Trausch, J.J. / Ceres, P. / Batey, R.T.
CitationJournal: Structure / Year: 2011
Title: The structure of a tetrahydrofolate-sensing riboswitch reveals two ligand binding sites in a single aptamer.
Authors: Trausch, J.J. / Ceres, P. / Reyes, F.E. / Batey, R.T.
History
DepositionJun 8, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2011Group: Database references
Revision 1.2Nov 2, 2011Group: Database references
Revision 2.0Nov 20, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_unobs_or_zero_occ_atoms
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.id / _chem_comp.name / _chem_comp.pdbx_synonyms / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id
Revision 2.1Feb 28, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tetrahydrofolate riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7947
Polymers28,8481
Non-polymers1,9456
Water1,856103
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)27.520, 68.590, 158.080
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: RNA chain Tetrahydrofolate riboswitch


Mass: 28848.162 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Synthesized from T7 RNA polymerase using a recombinant PCR template
#2: Chemical
ChemComp-IRI / IRIDIUM HEXAMMINE ION


Mass: 294.400 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: H18IrN6
#3: Chemical ChemComp-FFO / N-[4-({[(6S)-2-amino-5-formyl-4-oxo-3,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)benzoyl]-L-glutamic acid / [6S]-5-FORMYL-TETRAHYDROFOLATE / 6S-FOLINIC ACID


Mass: 473.439 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H23N7O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / Source method: isolated from a natural source / Formula: H2O

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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: 2.59 Å3/Da / Density % sol: 52.43 %
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2,4-methyl-pentanediol, spermine, sodium cacodylate, sodium chloride, dithiothreitol, pH 7.0, vapor diffusion, hanging drop, temperature 303K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.1051 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 4, 2010
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1051 Å / Relative weight: 1
ReflectionRedundancy: 3.5 % / Av σ(I) over netI: 16.9 / Number: 77168 / Rsym value: 0.027 / D res high: 1.955 Å / D res low: 62.895 Å / Num. obs: 22136 / % possible obs: 98.1
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
8.7462.986.910.0150.0152.9
6.188.7499.410.0140.0143.3
5.056.1899.110.0170.0173.3
4.375.0599.310.020.023.2
3.914.3798.710.0190.0193.3
3.573.9197.910.0190.0193.2
3.33.5797.510.020.023.3
3.093.397.310.0210.0213.5
2.913.099810.0260.0263.5
2.762.9199.210.0330.0333.5
2.642.7698.310.0470.0473.5
2.522.6499.910.0580.0583.5
2.422.5297.610.0810.0813.5
2.342.4299.510.1010.1013.6
2.262.349710.1360.1363.6
2.192.2698.710.1710.1713.5
2.122.1999.710.2280.2283.6
2.062.1294.610.2690.2693.6
2.012.0699.210.3410.3413.6
1.952.019810.4560.4563.7
ReflectionResolution: 1.95→62.922 Å / Num. all: 22136 / Num. obs: 22136 / % possible obs: 98.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Rsym value: 0.027 / Net I/σ(I): 20.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.95-2.013.70.4561.7574715720.45698
2.01-2.063.60.3412.3564115690.34199.2
2.06-2.123.60.2692.9536214920.26994.6
2.12-2.193.60.2283.4532914740.22899.7
2.19-2.263.50.1714.6513714580.17198.7
2.26-2.343.60.1365.7487813540.13697
2.34-2.423.60.1017.7490013720.10199.5
2.42-2.523.50.0819.6466113130.08197.6
2.52-2.643.50.05813.2445712580.05899.9
2.64-2.763.50.04715.8427012260.04798.3
2.76-2.913.50.03321.2397711280.03399.2
2.91-3.093.50.02619.9382411060.02698
3.09-3.33.50.02127.934419890.02197.3
3.3-3.573.30.0228.231369600.0297.5
3.57-3.913.20.01925.828729100.01997.9
3.91-4.373.30.01930.926738030.01998.7
4.37-5.053.20.0229.923037230.0299.3
5.05-6.183.30.01735.321306500.01799.1
6.18-8.743.30.01442.916635110.01499.4
8.74-62.8952.90.01539.57672680.01586.9

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Phasing

PhasingMethod: SAD
Phasing MADD res high: 1.95 Å / D res low: 79.04 Å / FOM : 0.365 / FOM acentric: 0.414 / FOM centric: 0.142 / Reflection: 22339 / Reflection acentric: 18232 / Reflection centric: 3252
Phasing MAD shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
9.09-12.770.420.6550.1261598767
7.44-9.090.4770.6550.16721213574
6.45-7.440.4560.6240.11424516478
5.77-6.450.5220.6520.225618370
5.27-5.770.4750.6190.13129420880
4.88-5.270.440.5610.15231222175
4.57-4.880.440.5770.1232022571
4.31-4.570.4350.5470.12836426877
4.09-4.310.4570.5760.11736927479
3.9-4.090.4530.570.11736927369
3.73-3.90.4150.5550.10841428581
3.58-3.730.4160.5780.11440726574
3.45-3.580.3790.4860.09241630068
3.34-3.450.3840.5080.07345532484
3.23-3.340.40.5010.09145834673
3.14-3.230.4360.510.10845737368
3.05-3.140.4680.5480.1147739175
2.97-3.050.4250.5030.09851541683
2.89-2.970.4260.4970.1253443378
2.82-2.890.4390.5120.1350741077
2.76-2.820.4380.4970.12751142866
2.7-2.760.4190.4840.12256545981
2.64-2.70.4140.4630.19755445671
2.59-2.640.4230.4830.14458047582
2.54-2.590.4020.4510.12356647970
2.49-2.540.4140.4620.16258348579
2.44-2.490.3750.4160.12259550370
2.4-2.440.3610.3930.15664355278
2.36-2.40.3720.4070.14460751767
2.32-2.360.350.3810.17162052580
2.29-2.320.3280.3460.19961654068
2.25-2.290.30.3240.14865254578
2.22-2.250.2910.3050.18765355770
2.19-2.220.3020.3220.15967358078
2.16-2.190.3160.3320.19567559273
2.13-2.160.2880.30.2268159081
2.1-2.130.2930.3070.17465457964
2.07-2.10.2720.2870.16971061078
2.05-2.070.2660.2780.16370660474
2.02-2.050.2890.3020.1972763977
2-2.020.2630.2760.14970962375
1.97-20.2830.2950.17872964874
1.95-1.970.260.2740.13572063975
Phasing dmFOM : 0.6 / FOM acentric: 0.61 / FOM centric: 0.55 / Reflection: 22342 / Reflection acentric: 19090 / Reflection centric: 3252
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
3.5-5.60.920.940.8730732440633
2.8-3.50.830.850.7137883196592
2.4-2.80.630.660.4237603268492
2.1-2.40.420.440.2966195868751
2-2.10.320.340.240613635426

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Processing

Software
NameVersionClassificationNB
SCALA3.3.15data scaling
PHASERphasing
RESOLVE2.15phasing
PHENIXdev_572refinement
PDB_EXTRACT3.1data extraction
BOSdata collection
XSCALEdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.95→62.895 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.7699 / SU ML: 0.32 / σ(F): 0.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2431 1962 8.9 %From phenix.refine
Rwork0.2294 ---
obs0.2307 22038 96.16 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 25.258 Å2 / ksol: 0.364 e/Å3
Displacement parametersBiso max: 324.69 Å2 / Biso mean: 40.1859 Å2 / Biso min: 16.87 Å2
Baniso -1Baniso -2Baniso -3
1-17.9289 Å2-0 Å20 Å2
2---6.9843 Å2-0 Å2
3---10.3856 Å2
Refinement stepCycle: LAST / Resolution: 1.95→62.895 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1913 57 103 2073
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022196
X-RAY DIFFRACTIONf_angle_d0.5023448
X-RAY DIFFRACTIONf_chiral_restr0.052446
X-RAY DIFFRACTIONf_plane_restr0.00492
X-RAY DIFFRACTIONf_dihedral_angle_d16.2721076
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.95-1.99470.37511290.3461294142390
1.9947-2.04860.33511360.32311368150494
2.0486-2.10890.32661290.31551354148391
2.1089-2.1770.33721360.31081377151396
2.177-2.25480.31941400.30831438157897
2.2548-2.34510.39191330.30311378151195
2.3451-2.45180.23651430.28381466160998
2.4518-2.58110.3271370.28061413155097
2.5811-2.74280.30831480.29521498164699
2.7428-2.95450.30521410.27721442158398
2.9545-3.25190.22631430.231466160998
3.2519-3.72240.24451440.21381476162098
3.7224-4.68960.17741500.17341526167698
4.6896-62.95510.18721530.18151580173396
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)
10.4674-0.0090.09110.8952-0.14480.19340.02170.04660.1102-0.0114-0.0504-0.12160.0466-0.0159-0.03390.54770.3889-0.08780.38480.10610.360610.344-16.971815.3993
20.01830.0147-0.04140.5624-0.28740.22090.03640.09590.04360.0583-0.0355-0.0026-0.0987-0.0669-0.06130.16610.10120.00830.23920.07440.11356.5979-1.66828.7864
30.315-0.02620.21150.2918-0.31010.50820.00090.22210.17730.1746-0.0265-0.007-0.12780.1289-0.11340.31030.08520.0260.3430.05310.236610.1873-10.590831.2087
40.0160.00340.00830.0237-0.00770.0127-0.0019-0.0066-0.03540.0539-0.0046-0.00270.09890.1005-0.01130.05210.1873-0.05960.34380.27250.22862.39649.17897.5665
50.09840.04020.07280.1119-0.03040.1029-0.00160.12360.0742-0.148-0.1060.03060.13930.0649-0.08710.65210.3776-0.03210.31410.00470.236113.4808-30.076718.0629
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESID 1:18
2X-RAY DIFFRACTION2CHAIN A AND RESID 19:35
3X-RAY DIFFRACTION3CHAIN A AND RESID 36:55
4X-RAY DIFFRACTION4CHAIN A AND RESID 56:71
5X-RAY DIFFRACTION5CHAIN A AND RESID 72:89

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