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- PDB-5fk1: SAM-I riboswitch bearing the H. marismortui Kt-7 variant 3bn is UG -

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Basic information

Entry
Database: PDB / ID: 5fk1
TitleSAM-I riboswitch bearing the H. marismortui Kt-7 variant 3bn is UG
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: 2.5 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 14, 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)32,70017
Polymers30,5841
Non-polymers2,11516
Water27015
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.580, 62.580, 154.730
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


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.: 3 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O
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: 2.06 Å3/Da / Density % sol: 40.27 % / Description: NONE
Crystal growpH: 7
Details: 40 MM NA-CACODYLATE (PH 7.0), 80 MM KCL, 50 MM BACL2, 12 MM SPERMINE-HCL, 10% (V/V) MPD.

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92
DetectorType: DECTRIS PIXEL / Detector: PIXEL / Date: Sep 24, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.5→77.36 Å / Num. obs: 11293 / % possible obs: 99.8 % / Observed criterion σ(I): 1.1 / Redundancy: 5.6 % / Biso Wilson estimate: 71.12 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 11.3
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 5.8 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 1.1 / % possible all: 99.7

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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: 2.5→58.015 Å / SU ML: 0.52 / σ(F): 1.34 / Phase error: 40.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.289 1076 5.4 %
Rwork0.2385 --
obs0.2414 11185 98.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 116.36 Å2
Refinement stepCycle: LAST / Resolution: 2.5→58.015 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2030 42 15 2087
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022305
X-RAY DIFFRACTIONf_angle_d0.6363593
X-RAY DIFFRACTIONf_dihedral_angle_d17.1871139
X-RAY DIFFRACTIONf_chiral_restr0.035475
X-RAY DIFFRACTIONf_plane_restr0.00596
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5003-2.61410.46091640.44322316X-RAY DIFFRACTION98
2.6141-2.75190.52121210.43982327X-RAY DIFFRACTION97
2.7519-2.92430.43181290.42542390X-RAY DIFFRACTION99
2.9243-3.15010.4316980.33222424X-RAY DIFFRACTION99
3.1501-3.4670.27491280.24232379X-RAY DIFFRACTION99
3.467-3.96860.30421490.21782348X-RAY DIFFRACTION98
3.9686-4.99960.23761210.18172404X-RAY DIFFRACTION100
4.9996-58.03040.24671660.20022354X-RAY DIFFRACTION99
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)
16.11553.62392.20287.29920.00491.1369-0.00060.4465-0.61522.8452-0.3657-0.3134-0.8914-2.28440.21650.96230.20230.05381.0847-0.17670.6072-0.5374-13.29530.8358
27.630.6304-1.63039.06012.38742.91170.9706-0.5254-1.62220.0805-0.93490.56081.4294-0.4185-0.06120.83810.2138-0.14771.47220.16040.718714.2761-14.23533.587
33.9707-1.01721.05480.8368-1.43766.68490.885-0.0271-0.2302-0.7174-0.11620.21570.8102-0.3982-0.57051.2691-0.1107-0.17781.55260.12670.943822.8332-7.922816.7587
48.036-1.7171-4.416.0308-3.19567.924-0.3367-0.2411.53914.059-0.3172-0.0404-0.45192.961.46752.6094-0.2676-0.13081.5561-0.45051.136117.65148.93527.2214
55.5309-3.348-1.10683.95274.50017.9747-0.1356-0.241.6131-0.14640.5604-0.3198-3.6162-1.7822-0.86672.58870.39480.40291.65610.09820.83532.76058.356831.1386
62.8657-0.13011.88538.63485.44584.8467-0.6038-1.0874-0.1265-0.1366-0.0063-0.06890.40940.92760.7951.1083-0.15130.07141.08130.08980.5852.1885-8.149826.6276
74.7416-2.47123.28528.59123.13948.07340.1559-0.18370.57431.54591.12060.55592.1181-2.3978-0.88741.3586-0.5152-0.02722.02970.09960.72112.4097-19.470827.1222
84.8368-0.60150.13382.58583.20888.0425-0.00030.2479-0.31431.46230.467-0.6478-0.1664-0.32880.08071.9089-0.44630.24731.250.09380.18117.999-7.628935.2649
94.56210.8107-1.33723.39261.82582.16260.85280.8341.1492-1.0827-0.2148-0.2398-1.66870.6421-0.34791.853-0.3570.24141.46490.04630.67737.04093.043730.3457
103.1535-1.4513-4.00771.64772.13255.050.63960.6250.5646-0.5715-0.19290.1736-1.92020.6205-0.4921.7104-0.39210.0441.3073-0.00080.729417.58476.994615.8245
117.08490.76213.27126.6369-0.70986.0388-0.0599-0.04920.3022-0.2186-0.4321-0.3401-2.52193.25430.69531.5463-0.22710.06061.6630.18780.515517.4389-0.18210.4555
121.40130.6357-2.29473.7018-1.78913.86080.74161.60260.67330.07410.0104-0.8508-2.36313.2454-0.06862.2235-0.46310.32652.21920.21270.767618.97649.43-1.3622
135.41821.43921.18516.54280.9685.95950.9083-0.38960.21670.5666-0.4174-0.0036-2.6074-0.8570.2451.8806-0.13860.18981.3951-0.07680.478112.26060.103112.4678
142.4093-0.8940.21973.5351-0.99292.1350.2504-0.6932-0.58030.72640.2457-0.681-0.0481-0.4443-0.29551.205-0.1811-0.14731.27370.20480.64715.5066-11.307822.7956
156.46810.59372.24093.53680.46366.88010.16970.2262-0.02370.43650.04780.74921.2119-0.87380.07841.0977-0.3469-0.22021.09770.10940.65469.2144-22.155621.6581
165.97821.41985.58966.6311-0.60626.7453-0.3964-0.0146-0.25530.877-0.19110.28062.28060.90140.35991.993-0.1298-0.24891.3343-0.06180.724214.6966-36.86615.2814
172.67940.95790.04284.9023-0.50515.20740.0847-0.2613-0.4388-1.7894-0.6554-0.35571.37910.19540.20411.6994-0.2763-0.16871.04690.13180.669417.9594-36.430125.4916
184.0573-4.5839-2.09535.65251.5932.5255-1.6220.1291-0.6650.38060.66050.70060.7706-0.80970.96941.4569-0.3576-0.05061.08340.05970.789612.733-26.066111.2591
197.13530.5342-0.60894.4126-0.27471.56520.42210.7777-0.2684-0.40650.56320.54570.084-0.1332-0.75450.89340.0143-0.07810.96580.03210.51297.0667-10.69457.6939
207.47772.31151.47113.76430.31582.9978-1.90460.9094-0.00020.6890.89770.7061-1.0845-0.97370.51511.05110.3891-0.04521.5324-0.28890.7429-0.7347-8.0265-6.2342
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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