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

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Basic information

Entry
Database: PDB / ID: 5fkh
TitleSAM-I riboswitch bearing the H. marismortui Kt-7 variant 3bn is CU
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: 2.65 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)32,67617
Polymers30,5441
Non-polymers2,13116
Water905
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.496, 62.496, 155.065
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

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RNA chain , 1 types, 1 molecules A

#1: RNA chain SAM-I RIBOSWITCH


Mass: 30544.314 Da / Num. of mol.: 1 / Fragment: SAM BINDING DOMAIN / Source method: obtained synthetically
Source: (synth.) THERMOANAEROBACTER TENGCONGENSIS (bacteria)

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Non-polymers , 5 types, 21 molecules

#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.: 1 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsNOTE MUTATION 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: 2.05 Å3/Da / Density % sol: 40.04 % / 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: ESRF / Beamline: ID23-1 / Wavelength: 0.9793
DetectorType: DECTRIS PIXEL / Detector: PIXEL / Date: Feb 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.65→42.5 Å / Num. obs: 9323 / % possible obs: 98.7 % / Observed criterion σ(I): 1.7 / Redundancy: 3.1 % / Biso Wilson estimate: 88.69 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 16.6
Reflection shellResolution: 2.65→2.78 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 1.7 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
HKLdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5FJC

5fjc


Resolution: 2.65→42.499 Å / SU ML: 0.47 / σ(F): 1.33 / Phase error: 36.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2775 751 4.8 %
Rwork0.2307 --
obs0.2329 9323 92.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 134.03 Å2
Refinement stepCycle: LAST / Resolution: 2.65→42.499 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2028 42 5 2075
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022302
X-RAY DIFFRACTIONf_angle_d0.6213589
X-RAY DIFFRACTIONf_dihedral_angle_d15.9641139
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 (%)
2.6502-2.85480.42041630.4223072X-RAY DIFFRACTION94
2.8548-3.1420.40681350.33673009X-RAY DIFFRACTION93
3.142-3.59640.29551650.23962985X-RAY DIFFRACTION93
3.5964-4.53030.26271700.23672971X-RAY DIFFRACTION92
4.5303-42.50460.24431180.19272925X-RAY DIFFRACTION89
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)
18.5907-1.2635.19836.1916-3.54174.41010.91873.4893-0.676-1.5096-0.6086-0.7251-1.963-1.2143-0.05921.21720.49260.02031.3291-0.06110.611713.70160.7386-0.867
29.5669-5.2497-6.5412.93973.62244.5193-1.6091-0.0995-0.8485-0.26930.3586-2.98851.64680.44020.85151.58890.16970.13280.7385-0.07320.879214.4571-13.9738-3.8706
30.4852-0.81610.69193.46480.24313.1402-1.64651.2007-1.44541.20210.93210.01721.00222.0841-0.15812.2047-0.50980.97731.9401-1.26561.33747.9808-22.1997-17.3081
43.0847-1.3228-4.32011.39822.10056.115-0.01050.6233-0.9952-1.491-0.42731.05773.60030.0275-1.71892.7289-0.855-0.36894.803-1.22610.6677-8.9544-15.8726-27.5706
51.9786-2.20031.77074.8863-3.63662.66712.88950.6511.02850.3942-0.32662.7435-4.0936-5.1411-2.1832.51630.72190.44513.20060.20711.0993-8.1264-1.3342-31.1108
67.75780.68851.51574.25291.6190.81310.97840.7110.3936-0.1827-0.7020.4758-1.0757-0.9936-0.32211.5705-0.07710.32451.40280.28711.07977.9104-1.5352-26.5268
78.73982.56437.77725.89922.71876.92832.73190.98342.86831.4796-1.86720.8629-2.19941.7512-0.64742.7248-0.21870.46061.23910.28061.297919.3579-1.7805-27.1053
84.38921.65591.5454.67052.98642.3573-1.11841.3709-2.24640.60461.8173-1.51421.798-1.33080.411.7199-0.29030.29751.92470.57830.46647.4962-7.5601-35.3136
93.03291.76162.77586.37853.93723.5809-1.684-1.1269-1.5340.64050.12610.50513.03462.65211.34821.62230.06780.39722.68410.271.1264-3.2257-5.9455-29.9056
107.4023.46323.78621.69561.76071.92360.67251.0818-1.9519-0.4274-0.75610.37320.7085-3.2527-0.04021.6211-0.09970.21082.6493-0.52820.6312-7.211-16.5203-16.0421
115.01192.46344.89511.25252.4034.99051.6944-1.1972-0.90320.5453-0.75750.30612.0587-0.6099-0.60382.0143-0.21950.26971.17040.01760.50680.2402-17.1585-0.6947
122.2170.5758-0.14785.4935-3.5342.2887-0.4475-2.2630.2729-0.4041-1.00581.37444.0103-2.26080.51822.5159-0.63730.42972.23730.3950.7667-9.3773-18.71911.1913
135.4556-0.7509-5.94773.47013.44878.4783-1.70172.02380.4687-2.15261.18830.9993-0.3084-1.76260.36251.5191-0.13410.01641.52890.04770.4221-0.0828-11.541-12.4545
142.4995.3876-2.11441.9554-4.51471.70940.05671.8029-0.3177-2.0548-1.0563-3.50210.0865-1.15330.82322.07290.28530.58591.4563-0.15410.55811.4301-14.9583-22.6781
154.64423.72135.72246.58243.08367.6928-0.54170.55140.5812-0.29830.4455-1.07-1.69620.40270.09862.0016-0.17630.66251.1003-0.30111.177622.2064-8.5707-21.6884
163.4135-3.5256-2.31753.82481.91275.7131-0.32871.05691.05362.01440.6525-1.4506-0.66861.73480.57381.5418-0.0195-0.33722.7172-0.58170.544637.1353-14.3393-15.3843
177.7175-1.5582-2.45112.99811.35952.16450.0335-2.1961.11640.62290.6516-1.0130.16782.5415-0.58080.8677-0.1986-0.03361.7904-0.37160.759636.3964-17.6238-25.6451
187.1775-6.0730.51265.2385-0.44676.40782.2469-0.58731.6453-1.3652-2.5421-0.64090.29230.8205-0.03251.4255-0.24760.5361.54-0.16831.232226.6216-12.5322-10.9976
197.66112.72340.79027.2979-3.46982.6563-0.34440.28720.8391-0.03591.2906-1.8710.09970.2135-1.05161.0375-0.03960.15370.6928-0.19030.882810.9865-6.7498-7.5204
205.12711.2270.74544.90880.16056.75020.0854-0.69850.5989-0.3025-2.2539-0.4282-1.4246-1.57241.39131.41350.3342-0.24950.76680.03740.61948.38090.88956.3043
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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