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- PDB-2qwy: SAM-II riboswitch bound to S-adenosylmethionine -

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Basic information

Entry
Database: PDB / ID: 2qwy
TitleSAM-II riboswitch bound to S-adenosylmethionine
ComponentsSAM-II riboswitch
KeywordsRNA / mRNA / riboswitch / SAM / S-adenosylmethionine / AdoMet / RNA-ligand complex / double helix / pseudoknot / base triple
Function / homology: / PHOSPHATE ION / S-ADENOSYLMETHIONINE / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SIRAS / Resolution: 2.8 Å
AuthorsGilbert, S.D. / Rambo, R.P. / Van Tyne, D. / Batey, R.T.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2008
Title: Structure of the SAM-II riboswitch bound to S-adenosylmethionine.
Authors: Gilbert, S.D. / Rambo, R.P. / Van Tyne, D. / Batey, R.T.
History
DepositionAug 10, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_leaving_atom_flag / _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-II riboswitch
B: SAM-II riboswitch
C: SAM-II riboswitch
A: PHOSPHATE ION
B: PHOSPHATE ION
C: PHOSPHATE ION
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,51815
Polymers50,4633
Non-polymers2,05512
Water2,774154
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A: SAM-II riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,5676
Polymers16,8211
Non-polymers7465
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SAM-II riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4094
Polymers16,8211
Non-polymers5883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: SAM-II riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,5425
Polymers16,8211
Non-polymers7214
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)115.258, 48.095, 109.617
Angle α, β, γ (deg.)90.00, 108.25, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe deposited coordinates contain all information corresponding to one biologically relevant unit repeated three times according to the number of RNA-ligand complexes observed in the asymmetric unit.

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Components

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RNA chain , 1 types, 3 molecules ABC

#1: RNA chain SAM-II riboswitch


Mass: 16821.043 Da / Num. of mol.: 3 / Source method: obtained synthetically
Details: The sequence was engineered based on the SAM-II riboswitch found upstream of the metX gene derived from a Sargasso Sea environmental sequence (Env12).

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Non-polymers , 5 types, 166 molecules ABC

#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cs
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C15H22N6O5S
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsEACH RNA MONOMER CONTAINS A 5'-DIPHOSPHATE AND A 2',3'-CYCLIC PHOSPHATE. THESE RESIDUES HAVE BEEN ...EACH RNA MONOMER CONTAINS A 5'-DIPHOSPHATE AND A 2',3'-CYCLIC PHOSPHATE. THESE RESIDUES HAVE BEEN SEPARATED INTO STANDARD MONOPHOSPHATE NECLEOTIDE AND INDIVIDUAL PHOSPHATE DURING ENTRY PROCESSING AT THE PROTEIN DATA BANK, AND THE LINK RECORDS HAVE BEEN BUILT TO INDICATE THE CONNECTIONS.

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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: 2.86 Å3/Da / Density % sol: 56.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 640 mM Ammonium Acetate, 10% PEG 1000, 10 mM Barium Chloride, 50 mM Sodium Cacodylate, 8 mM Cobalt Hexaammine Chloride. Micro-seeded., pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1Sodium Cacodylate11
2Ammonium Acetate11
3PEG 100011
4Barium Chloride11
5Cobalt Hexaammine Chloride11
6Sodium Cacodylate12
7Ammonium Acetate12
8PEG 100012
9Barium Chloride12
10Cobalt Hexaammine Chloride12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorDate: Apr 10, 2007
RadiationMonochromator: Nickel Filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. all: 27442 / Num. obs: 26866 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 7.8 % / Biso Wilson estimate: 129.5 Å2 / Rsym value: 0.061 / Net I/σ(I): 31.9
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 7.7 % / Mean I/σ(I) obs: 5 / Num. unique all: 4033 / Rsym value: 0.349 / % possible all: 94.7

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Processing

Software
NameVersionClassification
CNS1.2refinement
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: SIRAS / Resolution: 2.8→19.9 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1022121.53 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.263 1924 7.2 %RANDOM
Rwork0.206 ---
obs0.206 26866 97.9 %-
all-26866 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 9.21319 Å2 / ksol: 0.25 e/Å3
Displacement parametersBiso mean: 65.6 Å2
Baniso -1Baniso -2Baniso -3
1-34.88 Å20 Å223.73 Å2
2---5.03 Å20 Å2
3----29.85 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.5 Å0.4 Å
Luzzati d res low-5 Å
Luzzati sigma a0.62 Å0.62 Å
Refinement stepCycle: LAST / Resolution: 2.8→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 3354 105 154 3613
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.4
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.8→2.97 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.408 324 7.4 %
Rwork0.407 4033 -
obs--94.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep_revise4.paramdna-rna_rep_revise4.top
X-RAY DIFFRACTION3water_rep.paramwater_rep.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5sam7.paramsam7.top

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