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

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Basic information

Entry
Database: PDB / ID: 5fkf
TitleSAM-I riboswitch bearing the H. marismortui Kt-7 variant 3bn is UC
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.ptnr3_symmetry / _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

Downloads & links

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Assembly

Deposited unit
A: SAM-I RIBOSWITCH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,71518
Polymers30,5441
Non-polymers2,17117
Water00
1
A: SAM-I RIBOSWITCH
hetero molecules

A: SAM-I RIBOSWITCH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,43036
Polymers61,0892
Non-polymers4,34134
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area8140 Å2
ΔGint-293.9 kcal/mol
Surface area28460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.810, 61.810, 154.940
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: 30544.312 Da / Num. of mol.: 1 / Fragment: SAM BINDING DOMAIN / Source method: obtained synthetically
Source: (synth.) THERMOANAEROBACTER TENGCONGENSIS (bacteria)
#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


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.: 12 / 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.: 2 / 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: 2.01 Å3/Da / Density % sol: 38.9 % / Description: NONE
Crystal growpH: 7
Details: 40 MM NA-CACODYLATE (PH 7.0), 80 MM KCL, 50 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: 1
DetectorType: DECTRIS PIXEL / Detector: PIXEL / Date: Dec 8, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→77.47 Å / Num. obs: 7923 / % possible obs: 100 % / Observed criterion σ(I): 2.9 / Redundancy: 6.2 % / Biso Wilson estimate: 61.51 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 10.5
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.9 / % 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 5FJC

5fjc


Resolution: 2.8→57.41 Å / SU ML: 0.44 / σ(F): 1.34 / Phase error: 32.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2575 743 5.3 %
Rwork0.2045 --
obs0.2073 7923 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 77.13 Å2
Refinement stepCycle: LAST / Resolution: 2.8→57.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2027 43 0 2070
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052301
X-RAY DIFFRACTIONf_angle_d0.9853586
X-RAY DIFFRACTIONf_dihedral_angle_d17.4321139
X-RAY DIFFRACTIONf_chiral_restr0.05475
X-RAY DIFFRACTIONf_plane_restr0.00896
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8001-3.01630.44491520.32272654X-RAY DIFFRACTION100
3.0163-3.31980.29731590.2362647X-RAY DIFFRACTION100
3.3198-3.80020.24481360.20412682X-RAY DIFFRACTION100
3.8002-4.78740.19511220.18132698X-RAY DIFFRACTION100
4.7874-57.42250.2471740.18472646X-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)
17.7135-7.1415-7.45456.70766.91347.28320.13390.34810.2111-0.0331-0.3176-0.45890.69320.61230.04110.41020.51120.16170.80580.27360.5406-13.4996-0.6617-0.9544
27.5531-1.2561-1.90897.3106-3.55949.5263-0.37940.25590.0019-0.5058-0.3980.29780.14990.09780.51780.81440.23350.00370.51840.13080.4284-14.315613.8756-3.8016
33.33390.6693-1.41782.3218-0.12590.6468-0.16091.14980.47890.00920.34640.2358-0.6318-1.14730.05821.14020.03-0.08311.18720.2260.5671-7.978722.1996-16.9245
45.02753.30052.56016.97084.78839.4553-0.66981.83891.2654-0.8041-0.47940.218-0.4816-1.76431.22180.9731-0.17060.152.0250.19081.03728.744917.7537-27.3583
51.977-1.0038-1.66895.7811-0.57686.44610.39740.2988-0.04890.52720.4096-1.59420.33752.232-0.72351.22640.1961-0.10051.6525-0.240.57488.37091.6942-31.1812
66.4492-0.453-4.7072.46750.95663.68790.19570.1567-0.1072-0.2376-0.1507-0.1971-0.17170.5950.0470.7078-0.0257-0.04350.7231-0.10580.2779-7.7791.7921-26.7256
72.1839-2.1138-1.99427.2007-0.55596.15710.2220.1349-0.57620.09830.19-0.06121.0637-0.4315-0.45961.037-0.2808-0.05971.1276-0.07540.5178-19.13291.9448-27.2819
81.0113-0.3159-1.71691.01760.75093.39470.00080.4125-0.084-0.25940.19790.0759-0.1349-0.1174-0.13360.7377-0.1327-0.00730.84610.0390.1767-7.31777.5572-35.3207
93.62730.36370.77923.6540.20876.7282-0.3617-0.34510.02520.0080.2562-0.2306-0.56570.91420.11180.9796-0.269-0.11861.2005-0.06260.41613.38386.44-30.2785
102.52160.2414-1.05790.39151.22755.82130.0520.2821-0.12770.23690.4226-0.21560.33920.9549-0.3590.8502-0.46020.02091.4999-0.07740.4547.140817.04-15.9717
114.88930.5761-0.81583.70930.1535.82460.0408-0.22170.1750.43220.0674-0.2811-0.62080.2717-0.02981.0274-0.1644-0.12190.9702-0.05460.3342-0.227317.2213-0.5186
120.18290.3160.56941.6241.65862.2476-0.1164-0.410.63290.37470.0547-0.1523-0.720.43630.11191.6989-0.2674-0.271.6215-0.39910.61399.090718.96061.3596
131.62230.1267-0.3392.40471.3271.1786-0.08690.15460.162-0.13830.0993-0.09210.07730.17580.00150.8482-0.0958-0.10391.3165-0.2504-0.17520.195611.6955-12.3191
140.69561.2523-2.0273.3394-2.21978.6842-0.4790.2950.53190.20430.1603-0.0078-0.7420.02860.39790.79730.1427-0.19140.9290.20380.5138-11.067214.9952-22.7806
151.94062.5068-3.28876.0783-2.42166.78350.0927-0.25610.0215-0.0014-0.1226-0.33880.7001-1.0541-0.00190.5546-0.1076-0.04970.84950.12920.4571-21.93258.6744-21.8232
160.2345-0.0267-0.31314.8524-5.15366.0024-0.3888-0.0961-0.42180.2496-0.0677-0.10990.67390.00690.35180.8797-0.12630.16991.61170.38620.3177-36.602713.9601-15.4994
170.55830.37130.87440.34450.41731.7352-0.116-0.43770.03140.02780.26780.44540.3093-1.1342-0.30180.7193-0.2773-0.13071.12170.23350.4321-36.024817.3429-25.5928
183.4873-2.6167-0.85376.54970.74482.4440.43530.70390.2582-1.087-0.79010.15230.5844-0.86980.30940.8335-0.1576-0.02591.08330.21910.2703-25.942412.1045-11.4659
194.6399-1.43413.48348.0733.06517.61930.0111-0.5151-0.31690.20040.2150.7198-0.2094-0.1728-0.02970.60690.1318-0.06720.44380.0840.3548-10.63646.6599-7.7101
201.73731.2745-0.58973.78240.60046.2815-0.12120.1986-0.26150.17550.02420.07390.42820.6195-0.00461.10620.21740.16550.6195-0.02370.2415-8.2954-1.05026.1785
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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