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- PDB-3gx3: Crystal structure of the T. tengcongensis SAM-I riboswitch varian... -

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Basic information

Entry
Database: PDB / ID: 3gx3
TitleCrystal structure of the T. tengcongensis SAM-I riboswitch variant U34C/A94G bound with SAH
ComponentsRNA (94-MER)
KeywordsRNA / kink-turn / four-way junction / pseudoknot / riboswitch
Function / homology: / S-ADENOSYL-L-HOMOCYSTEINE / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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: RNA (94-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,21112
Polymers30,5681
Non-polymers64211
Water21612
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.427, 62.427, 158.221
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: 30568.338 Da / Num. of mol.: 1 / Mutation: U34C, A94G / Source method: obtained synthetically
Details: the sequence is based on a naturally occurring sequence found in T. tengcongensis
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 2.52 Å3/Da / Density % sol: 51.22 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7
Details: 20 mM magnesium chloride, 80 mM potassium chloride, 12 mM spermine, 10% MPD, 40 mM cacodylate, pH 7.0, VAPOR DIFFUSION, HANGING DROP
Components of the solutions
IDNameCrystal-IDSol-ID
1magnesium chloride11
2potassium chloride11
3spermine11
4MPD11
5cacodylate11
6magnesium chloride12
7potassium chloride12
8spermine12
9MPD12
10cacodylate12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 19, 2009 / Details: osmic mirror
RadiationMonochromator: Ni filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.7→20 Å / Num. obs: 8993 / % possible obs: 98.3 % / Observed criterion σ(I): 2 / Redundancy: 6.74 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 15.7
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 7.06 % / Rmerge(I) obs: 0.369 / Mean I/σ(I) obs: 4.6 / % possible all: 97.6

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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: 2.7→19.741 Å / SU ML: 0.54 / σ(F): 2.2 / Phase error: 33.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2907 897 9.99 %
Rwork0.2311 --
obs0.237 8977 98.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 23.38 Å2 / ksol: 0.245 e/Å3
Displacement parametersBiso mean: 54.6 Å2
Refinement stepCycle: LAST / Resolution: 2.7→19.741 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2030 36 12 2078
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082304
X-RAY DIFFRACTIONf_angle_d2.63592
X-RAY DIFFRACTIONf_dihedral_angle_d30.0651323
X-RAY DIFFRACTIONf_chiral_restr0.232475
X-RAY DIFFRACTIONf_plane_restr0.00896
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.86880.45531440.42171298X-RAY DIFFRACTION98
2.8688-3.08960.34881450.34781309X-RAY DIFFRACTION98
3.0896-3.39910.33261470.23261330X-RAY DIFFRACTION98
3.3991-3.88770.32031490.22211337X-RAY DIFFRACTION99
3.8877-4.88570.27851510.19771363X-RAY DIFFRACTION99
4.8857-19.74170.22021610.18411443X-RAY DIFFRACTION98

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