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- PDB-3gx7: Crystal structure of the T. tengcongensis SAM-I riboswitch varian... -

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Basic information

Entry
Database: PDB / ID: 3gx7
TitleCrystal structure of the T. tengcongensis SAM-I riboswitch variant U34C/A94G mutant A6C/U7G/A87C/U88G bound with SAM
ComponentsRNA (94-MER)
KeywordsRNA / kink-turn / four-way junction / pseudoknot / riboswitch
Function / homologyS-ADENOSYLMETHIONINE / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsMontange, R.K. / Batey, R.T.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Discrimination between Closely Related Cellular Metabolites by the SAM-I Riboswitch.
Authors: Montange, R.K. / Mondragon, E. / van Tyne, D. / Garst, A.D. / Ceres, P. / Batey, R.T.
History
DepositionApr 1, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: RNA (94-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1438
Polymers30,5981
Non-polymers5447
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.630, 62.630, 159.615
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 RNA (94-MER)


Mass: 30598.371 Da / Num. of mol.: 1 / Mutation: U34C, A94G, A6C, U7G, A87C, U88G / Source method: obtained synthetically
Details: This sequence is derived from a naturally occurring sequence found in T. tengcongensis
#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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg

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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: 2.56 Å3/Da / Density % sol: 51.91 %
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 15 mM barium chloride, 30 mM potassium chloride, 40 mM cacodylate, 10% MPD, 12 mM spermine-HCl, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 303K
Components of the solutions
IDNameCrystal-IDSol-ID
1barium chloride11
2potassium chloride11
3cacodylateCacodylic acid11
4MPD11
5spermine-HCl11
6barium chloride12
7potassium chloride12
8cacodylateCacodylic acid12
9MPD12
10spermine-HCl12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 12, 2009
RadiationMonochromator: Ni filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.95→20 Å / Num. obs: 7157 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 6.66 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 13.3
Reflection shellResolution: 2.95→3.06 Å / Redundancy: 6.81 % / Rmerge(I) obs: 0.439 / Mean I/σ(I) obs: 3.7 / % possible all: 100

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHENIXmodel building
PHENIX(phenix.refine)refinement
CrystalCleardata reduction
CrystalCleardata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2GIS

2gis


Resolution: 2.95→19.952 Å / SU ML: 0.56 / σ(F): 0.04 / Phase error: 32.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2708 705 10.01 %
Rwork0.214 --
obs0.22 7040 97.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 64.963 Å2 / ksol: 0.242 e/Å3
Displacement parametersBiso mean: 80.7 Å2
Refinement stepCycle: LAST / Resolution: 2.95→19.952 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2032 33 0 2065
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042307
X-RAY DIFFRACTIONf_angle_d1.8893598
X-RAY DIFFRACTIONf_dihedral_angle_d29.1841323
X-RAY DIFFRACTIONf_chiral_restr0.171475
X-RAY DIFFRACTIONf_plane_restr0.00596
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.95-3.17710.36321350.33011228X-RAY DIFFRACTION98
3.1771-3.49530.38721390.26651226X-RAY DIFFRACTION98
3.4953-3.99750.28121380.21981246X-RAY DIFFRACTION98
3.9975-5.02320.28491410.19151284X-RAY DIFFRACTION99
5.0232-19.95230.21281520.18491351X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 52.2568 Å / Origin y: 52.8597 Å / Origin z: 23.6506 Å
111213212223313233
T0.4449 Å20.0515 Å20.0281 Å2-0.4741 Å2-0.1062 Å2--0.5472 Å2
L1.4647 °21.6266 °21.5831 °2-0.3504 °21.5004 °2--5.1104 °2
S0.1548 Å °-0.1497 Å °-0.054 Å °-0.2115 Å °0.0057 Å °-0.1347 Å °-0.3224 Å °0.4421 Å °-0.1049 Å °
Refinement TLS groupSelection details: all

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