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- PDB-3dio: Crystallization of the Thermotoga maritima lysine riboswitch boun... -

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Basic information

Entry
Database: PDB / ID: 3dio
TitleCrystallization of the Thermotoga maritima lysine riboswitch bound to lysine, IRIDIUM HEXAMINE SOAK
ComponentsRNA (174-MER)
KeywordsRNA / riboswitch / lysine
Function / homologyIRIDIUM HEXAMMINE ION / : / LYSINE / RNA / RNA (> 10) / RNA (> 100)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å
AuthorsSerganov, A.A.
CitationJournal: Nature / Year: 2008
Title: Structural insights into amino acid binding and gene control by a lysine riboswitch.
Authors: Serganov, A. / Huang, L. / Patel, D.J.
History
DepositionJun 20, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 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 / 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.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.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
X: RNA (174-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,09234
Polymers56,6361
Non-polymers5,45733
Water4,666259
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.918, 78.004, 140.835
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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RNA chain , 1 types, 1 molecules X

#1: RNA chain RNA (174-MER)


Mass: 56635.598 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: In vitro transcribed RNA from the Thermotoga maritima MSB8 asd gene

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Non-polymers , 6 types, 292 molecules

#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-IRI / IRIDIUM HEXAMMINE ION


Mass: 294.400 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: H18IrN6
#5: Chemical ChemComp-LYS / LYSINE


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N2O2
#6: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 259 / 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: 2.61 Å3/Da / Density % sol: 52.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.7
Details: 18% PEG4000, 0.1M sodium citrate, 20% isopropanol, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG400011
2sodium citrate11
3isopropanol11
4PEG400012
5sodium citrate12
6isopropanol12

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
31
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X29A11.105199
SYNCHROTRONNSLS X29A21.105516
SYNCHROTRONNSLS X29A31.085799
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 6, 2008
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.1051991
21.1055161
31.0857991
ReflectionResolution: 2.4→20 Å / Num. all: 24039 / Num. obs: 23799 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Rmerge(I) obs: 0.113 / Net I/σ(I): 23.9
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.539 / Mean I/σ(I) obs: 3.4 / Num. unique all: 2338 / % possible all: 97.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.4→20 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.916 / SU B: 13.348 / SU ML: 0.173 / Isotropic thermal model: tls / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.423 / ESU R Free: 0.257 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24319 1206 5.1 %RANDOM
Rwork0.20397 ---
all0.20595 22705 --
obs0.20595 22478 99.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.732 Å2
Baniso -1Baniso -2Baniso -3
1--0.24 Å20 Å20 Å2
2---1.38 Å20 Å2
3---1.62 Å2
Refine analyzeLuzzati coordinate error obs: 0.173 Å
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 3752 156 259 4167
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0214321
X-RAY DIFFRACTIONr_angle_refined_deg1.1932.9996842
X-RAY DIFFRACTIONr_dihedral_angle_3_deg7.085154
X-RAY DIFFRACTIONr_chiral_restr0.0660.2870
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021838
X-RAY DIFFRACTIONr_nbd_refined0.1540.21493
X-RAY DIFFRACTIONr_nbtor_refined0.2640.22551
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.120.2375
X-RAY DIFFRACTIONr_metal_ion_refined0.0970.29
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1270.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.120.218
X-RAY DIFFRACTIONr_mcbond_it0.2871.55
X-RAY DIFFRACTIONr_mcangle_it0.45627
X-RAY DIFFRACTIONr_scbond_it0.87734558
X-RAY DIFFRACTIONr_scangle_it1.3724.56835
LS refinement shellResolution: 2.4→2.462 Å / Rfactor Rfree error: 0.257 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.451 78 -
Rwork0.308 1615 -
obs-1745 97.24 %

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