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- PDB-5fk3: SAM-I riboswitch bearing the H. marismortui Kt-7 variant 3bn is CC -

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Basic information

Entry
Database: PDB / ID: 5fk3
TitleSAM-I riboswitch bearing the H. marismortui Kt-7 variant 3bn is CC
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)33,11920
Polymers30,5431
Non-polymers2,57619
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.262, 62.262, 153.780
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: 30543.330 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.: 15 / Source method: obtained synthetically / Formula: Ba
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 2.03 Å3/Da / Density % sol: 39.45 % / Description: NONE
Crystal growpH: 7
Details: 40 MM NA-CACODYLATE (PH 7.0), 80 MM KCL, 10 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: 0.9794
DetectorType: DECTRIS PIXEL / Detector: PIXEL / Date: Aug 5, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.5→76.89 Å / Num. obs: 11159 / % possible obs: 100 % / Observed criterion σ(I): 1.9 / Redundancy: 11.3 % / Biso Wilson estimate: 71.11 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 13.1
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 11.3 % / Rmerge(I) obs: 0.09 / 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: WWPDB ENTRY 5FK2

5fk2


Resolution: 2.5→57.711 Å / SU ML: 0.43 / σ(F): 1.33 / Phase error: 36.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2678 1034 5.2 %
Rwork0.2063 --
obs0.2095 11084 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→57.711 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2028 45 14 2087
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022328
X-RAY DIFFRACTIONf_angle_d0.6773632
X-RAY DIFFRACTIONf_dihedral_angle_d15.771154
X-RAY DIFFRACTIONf_chiral_restr0.035480
X-RAY DIFFRACTIONf_plane_restr0.00597
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5004-2.63220.42231360.38822700X-RAY DIFFRACTION100
2.6322-2.79710.44421450.37052703X-RAY DIFFRACTION100
2.7971-3.01310.38941250.31062719X-RAY DIFFRACTION100
3.0131-3.31620.32721600.23582696X-RAY DIFFRACTION100
3.3162-3.7960.29191390.2032703X-RAY DIFFRACTION100
3.796-4.78220.23171770.16882682X-RAY DIFFRACTION100
4.7822-57.72680.20391520.16512702X-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)
15.0307-2.5523-4.21880.91872.27586.3698-1.38070.28440.7092.92441.1651-2.0825-0.6968-3.06850.30031.00550.3805-0.1110.7928-0.12311.0673-0.548548.84371.054
20.14260.1654-0.87783.01281.17055.77161.0755-0.7879-0.81290.3799-1.1397-0.54471.5267-0.57130.71720.52770.2391-0.07721.0290.05680.674414.04148.03073.7532
35.1522.5835-3.15133.6716-1.28488.40410.29651.4842-0.1791-1.22110.68560.0989-0.88990.6173-0.49770.82480.1361-0.26820.89770.0220.578822.606953.443415.8872
41.42560.2587-0.20724.73584.90155.53380.32241.11921.18150.6617-0.2463-1.0350.42392.68790.08551.56980.0519-0.17311.0267-0.06640.896417.897771.065227.3425
55.8153-4.6763-2.95816.43690.07774.7016-0.87110.19731.16910.56951.146-0.7346-3.2515-2.5188-0.83031.85210.45720.05681.14450.02050.50231.986270.669330.873
66.6795-2.88532.75923.74221.19693.9468-1.1524-1.5215-0.15170.1290.86020.31860.8228-0.48120.44390.888-0.1842-0.0460.66410.01510.48671.845154.283326.444
78.7602-1.2779-1.59889.1464-0.63847.2316-0.5467-0.15830.80950.65550.9391-0.01810.7637-0.8921-0.22460.8383-0.3054-0.0491.06020.03080.56342.25442.852427.0909
85.4892-0.81422.44456.66043.06437.7180.09840.3898-0.29510.7722-0.1361-0.04720.1064-0.025-0.06830.8135-0.1353-0.01930.7835-0.02540.37897.6154.953935.0197
97.11260.5414.78120.23190.47875.0642-0.2680.29420.3736-0.0113-0.3666-0.4316-1.67761.80830.55551.1899-0.13920.02850.65710.03560.52256.416165.742329.9139
105.1672-3.4091-0.08414.72913.25973.49770.79131.25530.4967-0.6723-1.028-0.0353-1.98910.17430.0461.3083-0.2572-0.06010.83760.0490.599717.409469.399115.8772
117.06961.86143.33793.2565-1.11634.7513-0.89430.88450.1628-0.1340.4912-0.3067-1.92272.14080.56111.1133-0.1157-0.07351.16970.21820.450117.26562.10470.4369
124.74141.4458-5.93766.5878-2.09117.6833-0.4890.35350.4109-0.56510.2179-0.896-2.5354.1673-0.09971.7929-0.40270.19292.21310.27580.711119.004471.3884-1.2877
139.5147-2.5717.99589.506-1.9336.67160.0199-0.55520.4740.6450.07930.0015-1.9093-0.4703-0.20961.05390.0090.08970.82140.02590.421312.143162.433412.3984
141.8049-0.0511-0.5025.336-2.71578.28880.29210.6991-0.54121.14810.008-0.7955-1.64740.31870.14710.7729-0.0392-0.15070.57720.05660.775215.300851.065422.6404
157.50491.57620.91054.04692.23917.2652-0.14140.18440.35240.20560.36110.33991.2638-1.5836-0.06770.795-0.2206-0.18260.7551-0.06030.54519.041740.129721.6825
163.5641.90313.07072.0684-0.15186.11750.0028-0.55950.29560.2418-0.69220.96841.9534-0.12830.63481.6999-0.1206-0.22840.803-0.13720.785214.505625.624415.3195
170.67160.2895-0.03512.9275-2.23072.00570.8347-0.2932-0.5179-0.8395-0.7399-0.24640.89160.5519-0.17131.3385-0.2181-0.25980.70410.10760.703317.69126.099625.4106
184.80830.71360.73310.86461.00191.9912-0.5288-0.6350.2328-0.02330.19620.36540.9032-0.38750.24240.9196-0.1208-0.09160.68360.05520.721512.462536.338411.2646
195.12764.0846-0.79966.9041-1.85937.2939-0.08380.3633-0.2625-0.54780.35970.37160.18170.1697-0.26060.49870.0842-0.09560.70460.03050.5386.863251.63847.7434
208.39883.19527.67299.849-0.67558.825-0.15321.5009-0.5511.48130.55821.139-1.3573-0.00340.11060.64820.2531-0.03841.3306-0.2110.6934-0.989554.0661-6.1211
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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