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- PDB-5fk2: SAM-I riboswitch bearing the H. marismortui Kt-7 variant 3bn is GG -

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Basic information

Entry
Database: PDB / ID: 5fk2
TitleSAM-I riboswitch bearing the H. marismortui Kt-7 variant 3bn is GG
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: 2.6 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 1.2Sep 6, 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_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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

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Assembly

Deposited unit
A: SAM-I RIBOSWITCH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,53213
Polymers30,6231
Non-polymers1,90912
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)61.480, 61.480, 153.750
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-2003-

HOH

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Components

#1: RNA chain SAM-I RIBOSWITCH


Mass: 30623.377 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.: 11 / Source method: obtained synthetically / Formula: Ba
#4: Water ChemComp-HOH / water / 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: 1.82 Å3/Da / Density % sol: 32.46 % / 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: 0.9763
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 4, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.6→76.87 Å / Num. obs: 9734 / % possible obs: 99.8 % / Observed criterion σ(I): 2.6 / Redundancy: 8.3 % / Biso Wilson estimate: 75.34 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 13.2
Reflection shellResolution: 2.6→2.72 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.98 / Mean I/σ(I) obs: 2.1 / % 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: 2.6→57.085 Å / SU ML: 0.48 / σ(F): 1.34 / Phase error: 37.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2726 904 5.2 %
Rwork0.2157 --
obs0.2187 9656 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 106.28 Å2
Refinement stepCycle: LAST / Resolution: 2.6→57.085 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2034 38 14 2086
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022310
X-RAY DIFFRACTIONf_angle_d0.6483603
X-RAY DIFFRACTIONf_dihedral_angle_d16.1311139
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 (%)
2.6002-2.76310.47071420.43362747X-RAY DIFFRACTION100
2.7631-2.97640.47131280.37682730X-RAY DIFFRACTION100
2.9764-3.27590.36271610.26422728X-RAY DIFFRACTION100
3.2759-3.74990.33011430.21942760X-RAY DIFFRACTION100
3.7499-4.72410.21641780.18552689X-RAY DIFFRACTION100
4.7241-57.0990.22371520.17592728X-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)
18.6356-3.21871.8848.71626.03256.63542.7699-2.5352-2.0229-0.099-2.7422-1.0799-2.7716-0.0769-0.14181.1375-0.54080.03170.9430.23930.835-13.28570.4659-37.5688
23.98443.86181.02339.5265-5.54567.4587-1.67920.43610.09810.8103-0.19931.6347-2.0433-1.40661.07021.3367-0.39210.06650.62330.14760.6031-14.0729-14.0294-34.7177
30.1159-0.1673-0.44958.5971-0.50932.03330.1680.4842-0.0651-0.5770.57470.59921.0793-1.0834-0.20461.015-0.06220.24571.02930.24870.8944-7.5098-22.4418-21.608
45.27410.6713-0.73821.86952.5773.9539-1.3794-3.25220.82580.58-0.2747-1.49372.13340.3829-0.21631.55560.4141-0.58342.1242-0.0411.05368.9505-16.6488-11.3354
52.75342.2771-2.14193.8939-1.56653.46881.63050.706-0.76260.389-1.4824-1.3198-2.33233.213-0.59461.2313-0.37080.152.4939-0.41050.79288.2297-1.8731-7.6812
67.83772.58593.61225.13791.14952.23870.25730.39130.57490.3494-0.7330.24790.76091.71460.59320.87540.08440.12640.770.04370.5579-8.0403-1.9587-12.0941
78.87861.43115.57632.2551-1.03195.17371.7647-1.04071.10940.39910.0655-0.4458-2.72-2.1898-0.28061.51450.38030.30970.7216-0.10910.6495-19.4286-2.2605-11.5345
83.49960.8491-0.23795.1987-0.37096.6659-0.3099-1.4087-0.1887-0.33220.5646-0.12820.260.4583-0.17850.93980.18940.01691.1228-0.03970.4698-7.4183-7.7039-3.4059
92.57710.44560.72851.53881.65512.0716-0.14561.0785-0.5256-0.40740.2337-0.14180.4539-1.11190.01491.06760.11680.10471.4459-0.22520.6763.3044-6.1673-8.6704
104.98341.78272.07922.00870.83935.1217-0.2937-0.4704-0.3967-0.90630.5719-0.59030.75852.55-0.00711.08630.34170.05311.5886-0.09980.72187.3871-16.7909-22.6714
113.5025-2.0905-1.89782.40690.08551.99430.46530.6189-0.2218-1.2482-0.6356-0.02161.84411.55130.25221.36410.01070.19741.18140.01220.49880.018-17.3253-37.8863
126.3544-3.1706-1.57114.93334.03743.55650.26490.5942-0.5199-1.1238-0.856-0.52334.2761-0.31850.12142.1543-0.05840.46951.3424-0.20360.92129.2564-19.0236-39.3839
132.6108-1.3152-2.04162.2467-0.63852.8243-0.56690.03550.2861-0.70651.1091-0.8659-0.0483.5619-0.4981.1456-0.14930.02711.2474-0.14640.57380.3255-11.793-25.912
140.20850.0694-0.72923.0679-0.31892.13620.2198-0.6745-0.1186-0.5228-0.02710.0779-0.25080.8526-0.04380.9411-0.15210.19380.9130.15120.7841-11.128-15.2568-15.8345
156.5519-1.3812-1.20294.09-0.46683.4004-0.6938-0.40910.6183-0.3161-0.0384-0.5138-0.5594-0.78890.21531.04190.1060.0030.73230.11620.5976-22.0864-9.0848-16.9498
165.3963-2.0901-1.76188.1952-4.72524.487-1.3298-0.98221.4620.41070.74280.24430.6395-2.91270.26031.10220.1009-0.00421.520.21340.6478-36.5465-14.6449-23.2626
174.8987-0.3589-1.68813.4341.61483.2817-0.77511.2072-0.54590.75820.43090.84940.1454-2.4210.06970.85760.26760.15541.45250.12080.6189-35.8993-17.7995-13.2247
184.37851.3993-1.34462.1491-1.18965.76340.55161.49141.21551.0601-0.24732.2043-1.1657-1.3572-0.32861.06110.16910.24670.96930.07680.9461-25.7913-12.59-27.3722
192.4321-1.2877-2.85573.33750.03527.194-0.03361.33641.4184-0.63780.23860.2019-0.8259-0.0076-0.16310.7729-0.16950.09990.59270.10010.6699-10.637-6.8275-30.7522
202.5873-2.00921.36573.8785-1.81.23110.9265-1.81370.768-0.5725-1.63080.69550.43661.12580.35981.3799-0.3138-0.09810.76820.02920.6857-8.00321.0602-44.5623
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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