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- PDB-4aob: SAM-I riboswitch containing the T. solenopsae Kt-23 in complex wi... -

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Basic information

Entry
Database: PDB / ID: 4aob
TitleSAM-I riboswitch containing the T. solenopsae Kt-23 in complex with S- adenosyl methionine
ComponentsSAM-I RIBOSWITCH
KeywordsTRANSLATION / K-TURN / RNA
Function / homology: / : / S-ADENOSYLMETHIONINE / RNA / RNA (> 10)
Function and homology information
Biological speciesTHERMOANAEROBACTER TENGCONGENSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsSchroeder, K.T. / Daldrop, P. / McPhee, S.A. / Lilley, D.M.J.
CitationJournal: RNA / Year: 2012
Title: Structure and Folding of a Rare, Natural Kink Turn in RNA with an Aa Pair at the 2B2N Position.
Authors: Schroeder, K.T. / Daldrop, P. / Mcphee, S.A. / Lilley, D.M.J.
History
DepositionMar 25, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 9, 2012Provider: repository / Type: Initial release
Revision 1.1May 30, 2012Group: Other
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_sf / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.ptnr3_symmetry / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _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)33,34529
Polymers30,4821
Non-polymers2,86328
Water18010
1
A: SAM-I RIBOSWITCH
hetero molecules

A: SAM-I RIBOSWITCH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,69158
Polymers60,9652
Non-polymers5,72656
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area13500 Å2
ΔGint-425.2 kcal/mol
Surface area27610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.300, 61.300, 157.538
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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RNA chain , 1 types, 1 molecules A

#1: RNA chain SAM-I RIBOSWITCH


Mass: 30482.281 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: STRUCTURE OF THE APTAMER DOMAIN
Source: (synth.) THERMOANAEROBACTER TENGCONGENSIS (bacteria)

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Non-polymers , 5 types, 38 molecules

#2: Chemical
ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Ba
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: K
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


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


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsMUTATIONS WERE ON THE FOLLOWING RESIDUES OF THE RNA SEQUENCE: U17G,G18C,G19A,G22A,C30U,C31U,A37C,A38C

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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: 2.42 Å3/Da / Density % sol: 65.61 % / Description: NONE
Crystal growpH: 7
Details: 40 MM NA-CACODYLATE PH 7, 80 MM KCL, 30 MM BACL2, 12 MM SPERMINE HCL 8%(V/V) MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 28, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 2.95→50 Å / Num. obs: 6810 / % possible obs: 98.5 % / Observed criterion σ(I): 3 / Redundancy: 9.5 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 26.8
Reflection shellResolution: 2.95→3.06 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 3.05 / % possible all: 89.5

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
HKL-2000data reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3GX5

3gx5


Resolution: 2.95→50 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.914 / SU B: 21.851 / SU ML: 0.217 / Cross valid method: THROUGHOUT / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23943 313 4.7 %RANDOM
Rwork0.18906 ---
obs0.1914 6386 97.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 74.637 Å2
Baniso -1Baniso -2Baniso -3
1-46.09 Å20 Å20 Å2
2--46.09 Å20 Å2
3----92.19 Å2
Refinement stepCycle: LAST / Resolution: 2.95→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2024 54 10 2088
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0112298
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.5451.4823581
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1330.2381
X-RAY DIFFRACTIONr_gen_planes_refined0.0230.021004
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.948→3.025 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 12 -
Rwork0.278 400 -
obs--85.83 %
Refinement TLS params.Method: refined / Origin x: 10.0705 Å / Origin y: 9.2057 Å / Origin z: 23.1604 Å
111213212223313233
T0.1466 Å20.0306 Å20.0039 Å2-0.1672 Å20.076 Å2--0.2715 Å2
L1.3361 °21.0493 °2-0.1753 °2-0.9646 °20.0188 °2--2.2081 °2
S0.1742 Å °-0.1907 Å °0.079 Å °0.0405 Å °-0.1118 Å °0.164 Å °0.0551 Å °0.2035 Å °-0.0624 Å °

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