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- PDB-5fke: SAM-I riboswitch bearing the H. marismortui Kt-7 variant 3bn is GU -

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Basic information

Entry
Database: PDB / ID: 5fke
TitleSAM-I riboswitch bearing the H. marismortui Kt-7 variant 3bn is GU
ComponentsSAM-I RIBOSWITCH
KeywordsRNA / KINK TURN / RNA MOTIF / SAM-I RIBOSWITCH
Function / homology: / : / S-ADENOSYLMETHIONINE / RNA / RNA (> 10)
Function and homology information
Biological speciesTHERMOANAEROBACTER TENGCONGENSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsHuang, L. / Lilley, D.M.J.
CitationJournal: Nucleic Acids Res. / Year: 2016
Title: A Critical Base Pair in K-Turns Determines the Conformational Class Adopted, and Correlates with Biological Function.
Authors: Huang, L. / Wang, J. / Lilley, D.M.J.
History
DepositionOct 15, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 25, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 6, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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: SAM-I RIBOSWITCH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,26521
Polymers30,5841
Non-polymers2,68120
Water0
1
A: SAM-I RIBOSWITCH
hetero molecules

A: SAM-I RIBOSWITCH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,53042
Polymers61,1692
Non-polymers5,36140
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area10310 Å2
ΔGint-405.7 kcal/mol
Surface area28300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.670, 62.670, 154.430
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: RNA chain SAM-I RIBOSWITCH


Mass: 30584.338 Da / Num. of mol.: 1 / Fragment: SAM BINDING DOMAIN, RESIDUES 1-94 / Source method: obtained synthetically
Source: (synth.) THERMOANAEROBACTER TENGCONGENSIS (bacteria)
#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Chemical
ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Ba
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
Sequence detailsMUTATION A94G

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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: 2.05 Å3/Da / Density % sol: 40.13 % / Description: NONE
Crystal growpH: 7
Details: 40 MM NA-CACODYLATE (PH 7.0), 80 MM KCL, 25 MM BACL2, 12 MM SPERMINE-HCL, 14% (V/V) MPD

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763
DetectorType: DECTRIS PIXEL / Detector: PIXEL / Date: Feb 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.8→77.21 Å / Num. obs: 8015 / % possible obs: 99.9 % / Observed criterion σ(I): 0.8 / Redundancy: 9.9 % / Biso Wilson estimate: 90.32 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 8.3
Reflection shellResolution: 2.8→3.02 Å / Redundancy: 10.6 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 0.8 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5FK3

5fk3


Resolution: 2.8→58.071 Å / SU ML: 0.58 / σ(F): 1.34 / Phase error: 45.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3058 745 5.2 %
Rwork0.2466 --
obs0.2497 8015 98.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 176.27 Å2
Refinement stepCycle: LAST / Resolution: 2.8→58.071 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2031 46 0 2077
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032306
X-RAY DIFFRACTIONf_angle_d0.9433596
X-RAY DIFFRACTIONf_dihedral_angle_d14.6651139
X-RAY DIFFRACTIONf_chiral_restr0.051475
X-RAY DIFFRACTIONf_plane_restr0.01196
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8001-3.01630.5221180.45612737X-RAY DIFFRACTION98
3.0163-3.31980.38071650.35172655X-RAY DIFFRACTION97
3.3198-3.80010.38061300.27742717X-RAY DIFFRACTION98
3.8001-4.78740.2761760.23972685X-RAY DIFFRACTION99
4.7874-58.08320.27041560.20052727X-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)
12.00154.2557-7.28665.5814-5.46186.6586-2.1073-0.0288-0.1179-4.62480.5697-1.03841.8379-0.47650.80961.47380.02240.2882.34220.54811.14890.3138-13.725337.9318
23.3058-2.49323.33328.8874-4.17983.7793-1.043-1.4974-0.03150.078-0.0421-0.2538-0.89071.59711.10821.7643-0.366-0.38042.03470.34551.0983-14.3773-14.196635.0685
38.4425-0.95761.36838.4522-1.23735.22350.7962-0.5064-1.5309-1.96390.7418-0.7121.75290.9078-1.08891.68330.2398-0.11772.4799-0.40991.0805-22.8588-7.726721.4515
42.29851.9772-2.7991.9966-6.26775.0723-0.74441.25231.9094-2.37211.16450.2882-0.8164-3.2339-1.35863.75221.09110.12792.20280.72761.4756-16.94668.9611.5447
57.15020.07043.35248.1297-2.36124.404-1.70751.50331.27381.16420.684-0.4341-4.54580.53941.31173.7065-0.31450.42492.3779-0.16061.4269-2.45437.93897.472
66.6937-5.12042.24887.6713-4.61592.9739-0.9893-0.0085-0.21750.20320.3497-0.314-1.25450.10530.74771.75720.5485-0.17462.2182-0.00650.9445-2.2291-9.208711.9421
74.4267-0.7427-1.22642.69471.64921.1479-0.5665-0.38890.31420.47931.8802-1.03352.10855.58460.47732.01360.73050.17843.1576-0.04970.9871-2.3526-20.33811.9328
86.03793.3102-2.58879.4952-5.28613.2668-0.8352-1.0716-0.2578-1.3660.9553-0.09940.5567-0.2017-0.30241.8430.2135-0.03231.8548-0.01280.7038-8.5309-8.59783.752
97.19761.49153.65749.0458-0.32422.30021.38271.82420.2063-0.1197-1.81230.90330.45020.31920.1872.51920.44550.25162.0819-0.2371.0359-6.38953.02749.0892
105.2523-4.5963-1.5584.19230.68985.2351-0.8295-4.21190.3901-0.89940.79911.8803-2.360.3847-0.17772.23050.5967-0.13211.9290.08671.0392-17.24087.419122.7013
119.3849-6.313-2.05534.28121.14095.9560.2568-0.0021-0.14771.8849-1.70022.1309-2.2679-1.6821.98412.22860.41340.18262.2856-0.06340.8443-17.4248-0.186338.0158
126.53170.615-2.83233.61082.68093.5969-1.3247-1.414-1.29960.94751.11090.3050.0833-3.90180.14623.27091.12250.34873.6748-0.33470.7192-18.98659.397439.6563
138.1576-1.57811.94947.7218-1.12354.4930.1955-0.06060.69851.00810.7420.7446-1.6811-0.8324-1.32892.12920.22710.212.03820.16380.9229-12.09010.172325.9672
144.38542.8051.61143.83833.73234.1805-1.7371-1.60030.58-3.749-0.9140.7245-1.16830.07812.29372.7188-0.1168-0.25151.864-0.16330.8927-15.3698-11.423716.245
158.8781.72512.74748.6362-3.97683.30260.86610.3117-0.15820.197-1.3792-0.84392.88553.15340.13762.16940.3613-0.2412.01670.17370.9634-9.292-22.951617.4379
165.1957-0.31312.48070.20830.95087.371-0.7235-1.8624-1.4701-0.1565-0.378-0.14612.664-0.4887-0.5923.90710.173-0.55411.92880.5077-0.0477-15.2196-37.136223.5967
179.47893.8521-0.36397.3788-1.06580.1581-0.17222.0226-0.41.22160.3276-0.393.63910.62750.29992.68980.3807-0.22441.5128-0.2650.5493-18.0539-36.613613.4048
181.1361-0.4362-1.08522.9342-0.18951.1729-1.78880.8223-0.92190.41490.2518-0.13843.32631.16260.57783.1110.40190.04341.6146-0.59571.0744-13.1766-26.310827.7308
195.30481.839-1.42959.19515.50959.89450.1548-1.1824-0.20222.8693-0.1591-0.36742.1627-0.16550.29661.2465-0.0588-0.11971.45970.10190.5843-7.1534-10.868231.226
204.47094.12441.83974.05852.0541.2564-0.12360.2717-0.9548-0.0045-0.5402-0.91-2.8079-0.99890.7721.3417-0.4850.02822.18080.28670.83570.6963-7.977344.8832
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 1:4)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 5:8)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 9:12)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 13:16)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 17:20)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 21:24)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 25:28)
8X-RAY DIFFRACTION8(CHAIN A AND RESID 29:33)
9X-RAY DIFFRACTION9(CHAIN A AND RESID 34:39)
10X-RAY DIFFRACTION10(CHAIN A AND RESID 40:45)
11X-RAY DIFFRACTION11(CHAIN A AND RESID 46:49)
12X-RAY DIFFRACTION12(CHAIN A AND RESID 50:56)
13X-RAY DIFFRACTION13(CHAIN A AND RESID 57:60)
14X-RAY DIFFRACTION14(CHAIN A AND RESID 61:64)
15X-RAY DIFFRACTION15(CHAIN A AND RESID 65:69)
16X-RAY DIFFRACTION16(CHAIN A AND RESID 70:73)
17X-RAY DIFFRACTION17(CHAIN A AND RESID 74:80)
18X-RAY DIFFRACTION18(CHAIN A AND RESID 81:84)
19X-RAY DIFFRACTION19(CHAIN A AND RESID 85:90)
20X-RAY DIFFRACTION20(CHAIN A AND RESID 91:94)

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