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- PDB-4b5r: SAM-I riboswitch bearing the H. marismortui K-t-7 -

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Basic information

Entry
Database: PDB / ID: 4b5r
TitleSAM-I riboswitch bearing the H. marismortui K-t-7
ComponentsSAM-I RIBOSWITCH
KeywordsRNA / RIBOSWITCH / K-TURN
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
AuthorsDaldrop, P. / Lilley, D.M.J.
CitationJournal: RNA / Year: 2013
Title: The Plasticity of a Structural Motif in RNA: Structural Polymorphism of a Kink Turn as a Function of its Environment.
Authors: Daldrop, P. / Lilley, D.M.J.
History
DepositionAug 7, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 30, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2013Group: Database references
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 / _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

Downloads & links

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Assembly

Deposited unit
A: SAM-I RIBOSWITCH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,92721
Polymers30,6071
Non-polymers2,32020
Water0
1
A: SAM-I RIBOSWITCH
hetero molecules

A: SAM-I RIBOSWITCH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,85542
Polymers61,2152
Non-polymers4,64040
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area9760 Å2
ΔGint-284.7 kcal/mol
Surface area27220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.720, 58.720, 154.710
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: 30607.377 Da / Num. of mol.: 1 / Fragment: APTAMER DOMAIN, RESIDUES 1-94 / Source method: obtained synthetically
Source: (synth.) THERMOANAEROBACTER TENGCONGENSIS (bacteria)
#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Chemical
ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Ba
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: K
Sequence detailsMUTATIONS U17G, G22C, C30G, U34A, A94G

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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: 2.32 Å3/Da / Density % sol: 47 % / Description: NONE
Crystal growpH: 7
Details: 40 MM NA-CACODYLATE PH 7, 80 MM KCL, 12 MM SPERMINE HCL, 20 MM BACL2, 14 %(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→32 Å / Num. obs: 6230 / % possible obs: 99.9 % / Observed criterion σ(I): 3 / Redundancy: 8.7 % / Rmerge(I) obs: 0.18 / Net I/σ(I): 11.5
Reflection shellResolution: 2.95→3.11 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 3.7 / % possible all: 100

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Processing

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

3gx5


Resolution: 2.95→54.9 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.9 / SU B: 20.209 / SU ML: 0.204 / Cross valid method: THROUGHOUT / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.25195 287 4.6 %RANDOM
Rwork0.21913 ---
obs0.22056 5898 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.436 Å2
Baniso -1Baniso -2Baniso -3
1-9.83 Å20 Å20 Å2
2--9.83 Å20 Å2
3----19.66 Å2
Refinement stepCycle: LAST / Resolution: 2.95→54.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2033 46 0 2079
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0112309
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6851.4753601
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_restr0.1030.2381
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021013
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
Rfree0.316 21 -
Rwork0.321 408 -
obs--99.08 %
Refinement TLS params.Method: refined / Origin x: 8.0458 Å / Origin y: -11.3258 Å / Origin z: -16.5567 Å
111213212223313233
T0.0051 Å20.0011 Å20.0169 Å2-0.0086 Å2-0.0004 Å2--0.0602 Å2
L0.3566 °20.1324 °20.4365 °2-0.4905 °2-0.1037 °2--0.695 °2
S0.0031 Å °-0.051 Å °0.028 Å °0.0293 Å °0.0051 Å °0.0716 Å °-0.0142 Å °-0.0771 Å °-0.0082 Å °

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