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- PDB-3iqp: SAM-I riboswitch from T. tencongensis variant A94G apo form -

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Basic information

Entry
Database: PDB / ID: 3iqp
TitleSAM-I riboswitch from T. tencongensis variant A94G apo form
ComponentsSAM-I riboswitch
KeywordsRNA / riboswitch / SAM / kink-turn / psuedoknot
Function / homology: / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.9 Å
AuthorsMontange, R.K. / Batey, R.T.
CitationJournal: Structure / Year: 2010
Title: Free state conformational sampling of the SAM-I riboswitch aptamer domain.
Authors: Stoddard, C.D. / Montange, R.K. / Hennelly, S.P. / Rambo, R.P. / Sanbonmatsu, K.Y. / Batey, R.T.
History
DepositionAug 20, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 4, 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 / 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_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_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)31,94311
Polymers30,5691
Non-polymers1,37310
Water1,71195
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: SAM-I riboswitch
hetero molecules

A: SAM-I riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,88522
Polymers61,1392
Non-polymers2,74720
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area5910 Å2
ΔGint-219 kcal/mol
Surface area28550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.702, 62.702, 159.260
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: 30569.322 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Chemical
ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Ba
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 2.56 Å3/Da / Density % sol: 51.96 %
Crystal growTemperature: 293 K / Method: hanging drop / pH: 7 / Details: pH 7.0, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 4, 2006
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→19.91 Å / Num. obs: 18385 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 7.2 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 14.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obs% possible all
2.6-2.695.50.3614.499.8
2.69-2.87.10.3635100
2.8-2.937.240.3335.599.9
2.93-3.087.310.2426.7100
3.08-3.277.380.1788.4100
3.27-3.527.40.11711.2100
3.52-3.887.420.10312.8100
3.88-4.437.470.06818.2100
4.43-5.567.560.04726.5100
5.56-19.877.60.02841.2100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
d*TREK9.1SSIdata scaling
CNSrefinement
PDB_EXTRACT3.005data extraction
CrystalCleardata reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GIS

2gis


Resolution: 2.9→19.91 Å / Rfactor Rfree error: 0.008 / Occupancy max: 1 / Occupancy min: 1 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflection
Rfree0.271 1237 9.2 %
Rwork0.231 --
obs0.231 13401 99.9 %
all-13410 -
Solvent computationSolvent model: FLAT MODEL / Bsol: 23.95 Å2 / ksol: 0.25 e/Å3
Displacement parametersBiso mean: 56.47 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.63 Å0.58 Å
Refinement stepCycle: LAST / Resolution: 2.9→19.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2030 10 95 2135
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
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_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d18.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.57
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.381.5
X-RAY DIFFRACTIONc_mcangle_it0.672
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shellResolution: 2.9→3.08 Å / Rfactor Rfree error: 0.025
RfactorNum. reflection% reflection
Rfree0.367 210 9.4 %
Rwork0.336 2014 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1water_rep.paramdna-rna_rep_revise.top
X-RAY DIFFRACTION2ion2.paramion2.top
X-RAY DIFFRACTION3dna-rna_rep_revise.paramwater.top

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