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

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Basic information

Entry
Database: PDB / ID: 5fkg
TitleSAM-I riboswitch bearing the H. marismortui Kt-7 variant 3bn is CG
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: 2.95 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 1.2Sep 13, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 1.3Jan 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_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)32,93821
Polymers30,5841
Non-polymers2,35420
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.252, 61.252, 155.969
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-1105-

BA

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Components

#1: RNA chain SAM-I RIBOSWITCH


Mass: 30584.338 Da / Num. of mol.: 1 / Fragment: SAM BINDING DOMAIN (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.: 13 / Source method: obtained synthetically / Formula: Ba
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / 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

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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: 1.95 Å3/Da / Density % sol: 37.95 % / Description: NONE
Crystal growpH: 7
Details: 40 MM NA-CACODYLATE (PH 7.0), 80 MM KCL, 15 MM BACL2, 12 MM SPERMINE-HCL, 8 % (V/V) MPD

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.95→61.25 Å / Num. obs: 6751 / % possible obs: 100 % / Observed criterion σ(I): 1.9 / Redundancy: 9.5 % / Biso Wilson estimate: 75.51 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 9.7
Reflection shellResolution: 2.95→3.13 Å / Redundancy: 1.9 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 1.9 / % 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 5FK3

5fk3


Resolution: 2.95→57.013 Å / SU ML: 0.55 / σ(F): 1.34 / Phase error: 35.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2987 641 5.4 %
Rwork0.2337 --
obs0.2371 6751 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 114.91 Å2
Refinement stepCycle: LAST / Resolution: 2.95→57.013 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2031 46 0 2077
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052306
X-RAY DIFFRACTIONf_angle_d1.2133596
X-RAY DIFFRACTIONf_dihedral_angle_d15.0321139
X-RAY DIFFRACTIONf_chiral_restr0.058475
X-RAY DIFFRACTIONf_plane_restr0.01296
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9502-3.17790.42521370.37012258X-RAY DIFFRACTION100
3.1779-3.49770.31631030.29392269X-RAY DIFFRACTION100
3.4977-4.00370.28181220.23252260X-RAY DIFFRACTION100
4.0037-5.04380.28831450.21012237X-RAY DIFFRACTION100
5.0438-57.02340.27961340.20172255X-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)
16.84262.6678-2.70063.3793-1.97777.0903-1.13050.73420.318-2.05130.66830.2359-0.20480.73990.50831.4078-0.5106-0.16820.7667-0.09380.57480.6194-13.516438.4212
21.999-1.20931.04024.21610.9287.1564-0.013-0.9163-0.8533-0.1302-0.59820.72210.63410.32080.18230.9862-0.8643-0.40091.7809-0.19180.2414-14.1275-14.193635.3095
37.64830.6438-1.86046.70021.12134.87571.38460.5961-0.537-0.6555-0.17590.07982.4385-0.5886-0.98781.38650.1418-0.39331.5293-0.13610.693-21.5226-7.448721.3208
43.6076-0.56414.40034.02551.07597.1048-0.31540.51261.0402-0.7973-1.0212-0.5429-0.253-0.86841.4533.11010.6317-0.27952.49150.6240.8712-14.62538.947711.3031
54.31751.967-0.76345.5825-0.67445.35130.1762-0.09961.45440.68080.30030.5801-3.46870.0895-0.33283.7069-0.15150.34991.1419-0.16030.8544-0.80577.52138.172
68.95062.31550.75795.10213.66552.74-0.87250.2230.1124-1.37620.7034-0.3437-0.91161.1252-0.00831.2590.3095-0.10521.3217-0.51371.0247-1.7233-8.97913.6754
71.53620.19531.68130.03180.18461.8940.39260.7948-0.2551-0.29760.5075-0.7770.07970.6073-0.19151.27330.3440.1571.963-0.6481.2125-1.161-20.117613.2622
80.1239-0.01590.07610.186-0.00850.2185-0.1580.40080.0346-0.18970.1192-0.59780.15990.315-0.16251.7108-0.0940.45871.4472-0.36260.6457-7.1051-8.76894.5532
98.7693-0.7511.25255.1454-1.20330.68540.3613-0.1588-0.2025-1.3037-0.08130.4807-0.3122-0.0358-0.05171.86030.1722-0.0621.3746-0.31440.7822-4.67432.91759.6126
105.80842.5389-3.69685.92-1.75246.8562-0.057-0.95640.9383-1.2648-0.04210.3227-1.67520.4657-0.08631.50140.5562-0.07751.3143-0.25450.6879-15.79487.305522.715
112.919-0.4824-1.4265.75130.99472.4758-0.145-0.28940.12150.84020.0990.05520.10820.16390.05450.76670.14820.02821.812-0.33850.5572-17.16550.02637.9956
123.1858-2.2121-3.36412.90762.47893.572-0.35560.1315-0.0990.72980.25470.7125-0.3573-1.48120.12051.33380.14690.15612.1331-0.3630.7615-18.80279.758239.8392
136.16430.6933-0.32638.44411.59930.764-0.168-0.43010.3575-0.28040.1234-0.12150.23440.92170.32131.20780.00940.16831.2366-0.12920.4649-11.11820.1126.4609
143.3431.5362-0.86572.0342-0.06572.5273-0.3181-0.3617-0.2331-0.2686-0.43480.6142-0.0584-0.28070.57881.6358-0.5152-0.14091.4089-0.32860.1328-14.6159-11.57416.4277
155.411-2.7319-0.39373.84691.18390.5060.5343-0.2119-0.19890.4340.3759-0.78672.12331.2668-0.90811.62840.1914-0.30271.3832-0.21430.5442-8.2232-22.796618.2109
161.6234-0.16221.68170.6136-1.20825.1181-0.208-0.19330.03250.085-0.7402-0.27270.36030.9412-0.1553.31580.0457-0.85330.98120.7231-0.196-14.5632-37.014223.5821
170.96090.3641-0.44170.74860.08120.27870.887-0.1377-0.14180.50890.046-0.19120.62840.4544-0.04092.10170.3249-0.51020.76250.00280.442-17.3136-36.193613.2892
184.52262.0282-0.56355.6080.34682.2997-0.0461-0.14160.145-0.02870.10350.0910.5373-0.3234-0.01342.34520.2167-0.40280.7466-0.16980.7629-12.7353-26.466928.2454
192.2268-1.49680.40912.7971-3.23647.52581.16570.3813-0.541-0.13-0.6840.07192.1351-0.0099-0.54411.0011-0.0485-0.12050.9196-0.0640.4301-6.798-10.998931.6818
204.6672-3.05914.3465.1719-2.2365.6779-0.91850.84460.11250.2457-0.4097-0.9906-0.72510.54590.89990.7398-0.2858-0.06250.9730.03370.63950.6716-8.240645.2006
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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