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- PDB-5fk6: SAM-I riboswitch bearing the H. marismortui Kt-7 variant 3bn is CA -

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Basic information

Entry
Database: PDB / ID: 5fk6
TitleSAM-I riboswitch bearing the H. marismortui Kt-7 variant 3bn is CA
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 2.0Jan 10, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _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.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.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.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_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)32,71517
Polymers30,5511
Non-polymers2,16416
Water543
1
A: SAM-I RIBOSWITCH
hetero molecules

A: SAM-I RIBOSWITCH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,43034
Polymers61,1032
Non-polymers4,32732
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area7990 Å2
ΔGint-244.8 kcal/mol
Surface area28550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.170, 62.170, 153.359
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-1096-

BA

21A-2001-

HOH

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Components

#1: RNA chain SAM-I RIBOSWITCH


Mass: 30551.354 Da / Num. of mol.: 1 / Fragment: SAM BINDING DOMAIN / 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-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.: 3 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsA94G MUTATION

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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: 2.02 Å3/Da / Density % sol: 39.13 % / Description: NONE
Crystal growpH: 7
Details: 40 MM NA-CACODYLATE (PH 7.0), 80 MM KCL, 50 MM BACL2, 12 MM SPERMINE-HCL, 12% (V/V) MPD

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9763
DetectorType: DECTRIS PIXEL / Detector: PIXEL / Date: Oct 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.5→62.17 Å / Num. obs: 10933 / % possible obs: 99.7 % / Observed criterion σ(I): 1 / Redundancy: 8.8 % / Biso Wilson estimate: 79.22 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.1
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 9.2 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 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: 2.5→57.615 Å / SU ML: 0.56 / σ(F): 1.33 / Phase error: 43.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2755 1019 5.2 %
Rwork0.2135 --
obs0.2167 19660 98.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 134.47 Å2
Refinement stepCycle: LAST / Resolution: 2.5→57.615 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2028 42 3 2073
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022303
X-RAY DIFFRACTIONf_angle_d0.6163589
X-RAY DIFFRACTIONf_dihedral_angle_d15.5491139
X-RAY DIFFRACTIONf_chiral_restr0.032475
X-RAY DIFFRACTIONf_plane_restr0.00596
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5002-2.6320.58911240.47332693X-RAY DIFFRACTION99
2.632-2.79690.48681450.44872667X-RAY DIFFRACTION99
2.7969-3.01290.51571230.39412647X-RAY DIFFRACTION98
3.0129-3.3160.33641630.2562659X-RAY DIFFRACTION99
3.316-3.79580.32011360.2112680X-RAY DIFFRACTION100
3.7958-4.78190.24581780.17432634X-RAY DIFFRACTION98
4.7819-57.63080.20381500.16452661X-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)
19.1641-5.6954-5.15628.73315.41899.28590.41974.08670.20340.4057-3.18710.41111.89340.65541.87781.70980.1082-0.05181.74480.15551.0106-13.4587-0.7098-0.8149
27.8495-1.58120.80660.69741.30199.0975-1.4027-1.3104-0.41390.25630.50660.17042.20080.46290.14221.59830.30930.10281.25120.25870.8028-13.996414.1183-3.6484
32.56030.252.9699.6713-0.25324.7852-1.25783.19931.15250.49261.59940.5505-1.4585-0.2456-0.31951.4895-0.1109-0.17331.68970.23590.9784-7.444122.7204-16.9264
45.7744-4.9416-2.28165.63244.37484.7734-0.56865.7504-0.68970.0162-1.3078-0.3291-4.0582-0.33811.24382.332-0.3010.33923.0419-0.02961.25199.32716.2052-26.7223
58.66452.49042.40148.88293.88936.65462.8407-1.97570.4228-2.4152-0.7751-4.656-0.2284.1117-1.81391.94560.19520.07052.8211-0.71441.25988.54871.8157-30.9409
63.97961.3151-2.88755.3232-1.90913.70261.3292-0.27080.3128-1.0577-0.1664-0.01420.14790.7179-1.04271.0891-0.2272-0.0381.233-0.01260.808-8.32852.2399-26.2605
72.16980.86960.63148.249-1.54083.42281.542-0.3087-0.9144-0.1731-0.42410.15373.4885-1.8892-1.37912.2237-0.7131-0.11291.4830.02250.8297-19.88632.5805-26.7288
86.5349-2.5861-4.89586.685-0.2694.3468-0.48152.4275-0.59350.6632-0.10880.33580.37280.04760.34420.9488-0.30460.01171.2943-0.17390.5545-7.76637.9926-34.8873
94.8777-1.05110.67484.7062.77313.97790.308-1.12860.04741.01270.6085-0.8366-2.02652.6107-0.78091.3519-0.3194-0.12491.8425-0.13610.8013.29326.6108-29.846
107.9511-2.4066-5.11892.75724.29146.1141-0.4887-0.07630.55620.5361.7579-1.0565-0.00773.3627-0.84811.5176-0.3872-0.11082.06-0.11670.97317.432816.965-15.6417
115.97612.1159-1.56759.657-6.67574.91290.2609-0.791-0.07330.2660.1814-0.2565-2.37851.5139-0.56761.9376-0.2092-0.27221.582-0.0590.8343-0.108217.4289-0.5513
124.03512.3408-0.01253.82192.66935.9521.09550.16460.15061.3749-0.6018-1.0002-4.10251.3412-0.15932.8202-0.1252-0.45981.8525-0.10011.15729.405619.29760.931
132.28923.4987-2.32798.56450.99217.7503-0.47470.9413-0.48991.4290.6616-0.96581.28231.4913-1.18691.5201-0.0484-0.07811.4308-0.21850.84230.365911.9987-12.5639
145.08951.98933.58296.88731.26062.57240.9109-0.0371-0.21930.3666-0.7175-0.00690.76251.51580.61280.91780.0373-0.15621.1910.10190.7093-11.224415.5364-22.4607
157.9143-1.3175-3.86065.3219-0.87033.00010.93550.1462-0.79481.3189-0.92930.32572.8021-1.6633-0.43081.2584-0.3157-0.05031.48150.22550.661-22.36939.4627-21.2329
162.1221.24386.01734.1229-3.58442.0659-1.3902-0.0375-0.21980.27440.08130.2069-0.3181-3.0095-0.1521.3726-0.17670.00553.34350.01990.9241-36.715915.1869-15.0428
178.5328-1.6230.9077.12771.80510.3618-0.6729-0.9770.7255-0.75430.68640.63530.6828-1.7702-0.04171.297-0.2439-0.29172.46640.01690.8188-36.072118.2592-25.1266
183.5188-3.35861.1844.1917-2.88287.4716-0.2572-0.862-0.3132-1.66210.65811.64920.599-1.787-0.22241.2662-0.2114-0.09031.57920.0291.017-25.972613.1206-10.8017
193.4961.41214.48435.44540.58986.44890.8122-1.4189-1.02471.5099-0.0413-0.25211.026-0.9486-0.33811.23810.1344-0.03410.99920.14110.7072-10.59946.9827-7.5858
203.4064-3.9624-0.54915.71310.50040.08350.01970.0241-1.29912.8329-0.90280.3362-0.71140.4770.64642.00480.23080.11071.22960.1140.9829-7.9169-1.0476.0762
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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