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- PDB-2gis: Structure of the S-adenosylmethionine riboswitch mRNA regulatory ... -

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Basic information

Entry
Database: PDB / ID: 2gis
TitleStructure of the S-adenosylmethionine riboswitch mRNA regulatory element
ComponentsSAM-I riboswitch
KeywordsRNA / mRNA / riboswitch / s-adenosylmethionine / SAM / RNA-ligand complex
Function / homologyIRIDIUM HEXAMMINE ION / S-ADENOSYLMETHIONINE / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.9 Å
AuthorsMontange, R.K. / Batey, R.T.
CitationJournal: Nature / Year: 2006
Title: Structure of the S-adenosylmethionine riboswitch regulatory mRNA element.
Authors: Montange, R.K. / Batey, R.T.
History
DepositionMar 29, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_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

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Assembly

Deposited unit
A: SAM-I riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1788
Polymers30,5531
Non-polymers1,6257
Water1,58588
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.901, 62.901, 158.967
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 SAM-I riboswitch


Mass: 30553.322 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: This sequence was engineered based on the SAM-I riboswitch from the metF-metH operon in Thermoanaerobacter tengcongensis
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-IRI / IRIDIUM HEXAMMINE ION


Mass: 294.400 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: H18IrN6
#4: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 2.57 Å3/Da / Density % sol: 52.2 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.10532, 1.10573
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 11, 2005
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.105321
21.105731
ReflectionResolution: 2.9→49.32 Å / Num. all: 15002 / Num. obs: 14940 / % possible obs: 99.6 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 14.64 % / Biso Wilson estimate: 139.3 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 17.9
Reflection shellResolution: 2.9→3.08 Å / Redundancy: 11.74 % / Rmerge(I) obs: 0.426 / Mean I/σ(I) obs: 4.4 / % possible all: 99.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
BOSdata collection
d*TREKdata scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.9→49.32 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 441185.1 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.289 999 7.4 %RANDOM
Rwork0.266 ---
all0.266 13511 --
obs0.266 13415 99.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 300 Å2 / ksol: 0.880832 e/Å3
Displacement parametersBiso mean: 69.6 Å2
Baniso -1Baniso -2Baniso -3
1-11.87 Å20 Å20 Å2
2--11.87 Å20 Å2
3----23.74 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.35 Å0.39 Å
Refinement stepCycle: LAST / Resolution: 2.9→49.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2029 57 88 2174
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d17.3
X-RAY DIFFRACTIONc_improper_angle_d2.31
X-RAY DIFFRACTIONc_mcbond_it1.381.5
X-RAY DIFFRACTIONc_mcangle_it2.562
X-RAY DIFFRACTIONc_scbond_it1.632
X-RAY DIFFRACTIONc_scangle_it2.612.5
LS refinement shellResolution: 2.9→3.08 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.416 162 7.3 %
Rwork0.427 2056 -
obs--98.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1dna-rna_rep.paramdna-rna_rep.top
X-RAY DIFFRACTION2ion2.paramion2.top
X-RAY DIFFRACTION3sam3.paramsam3.top
X-RAY DIFFRACTION4water_rep.paramwater_rep.top

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