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

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Basic information

Entry
Database: PDB / ID: 3diq
TitleCrystallization of the Thermotoga maritima lysine riboswitch bound to homoarginine
ComponentsRNA (174-MER)
KeywordsRNA / riboswitch / Lysine
Function / homologyL-HOMOARGININE / : / RNA / RNA (> 10) / RNA (> 100)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / REFMAC / Resolution: 2.7 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 1.2Oct 21, 2020Group: Data collection / Derived calculations
Category: pdbx_struct_conn_angle / reflns_shell ...pdbx_struct_conn_angle / reflns_shell / struct_conn / struct_site
Item: _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id ..._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.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.value / _reflns_shell.Rmerge_I_obs / _reflns_shell.number_unique_obs / _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
Revision 1.3Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA (174-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,30813
Polymers56,6361
Non-polymers67312
Water77543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.746, 78.794, 140.069
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 A

#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 , 5 types, 55 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.: 9 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-HRG / L-HOMOARGININE


Type: L-peptide linking / Mass: 188.228 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H16N4O2
#5: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


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


Mass: 18.015 Da / Num. of mol.: 43 / 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: 2.62 Å3/Da / Density % sol: 53.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.7
Details: 18% PEG 4000, 0.1M Sodium Citrate, 20% isopropanol, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 400011
2Sodium Citrate11
3isopropanol11
4PEG 400012
5Sodium Citrate12
6isopropanol12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 16, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.7→20 Å / Num. all: 17041 / Num. obs: 16172 / % possible obs: 94.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Rmerge(I) obs: 0.119 / Net I/σ(I): 13.2
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2.4 / Num. unique all: 1662 / Num. unique obs: 1479 / % possible all: 89

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
RefinementMethod to determine structure: REFMAC
Starting model: pdb entry 3DIL

3dil


Resolution: 2.7→20 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.882 / SU B: 11.885 / SU ML: 0.247 / Isotropic thermal model: TLS / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.338 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24134 806 5 %RANDOM
Rwork0.20182 ---
all0.20384 16081 --
obs0.20384 15261 94.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.898 Å2
Baniso -1Baniso -2Baniso -3
1--1.03 Å20 Å20 Å2
2---0.63 Å20 Å2
3---1.66 Å2
Refine analyzeLuzzati coordinate error obs: 0.247 Å
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 3752 27 43 3822
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0214215
X-RAY DIFFRACTIONr_angle_refined_deg1.1812.9996575
X-RAY DIFFRACTIONr_chiral_restr0.0620.2870
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021843
X-RAY DIFFRACTIONr_nbd_refined0.1540.21589
X-RAY DIFFRACTIONr_nbtor_refined0.2660.22559
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.2187
X-RAY DIFFRACTIONr_metal_ion_refined0.0380.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1310.242
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.150.210
X-RAY DIFFRACTIONr_mcbond_it0.1161.55
X-RAY DIFFRACTIONr_mcangle_it0.26127
X-RAY DIFFRACTIONr_scbond_it0.72734451
X-RAY DIFFRACTIONr_scangle_it1.1654.56568
LS refinement shellResolution: 2.7→2.769 Å / Rfactor Rfree error: 0.338 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.385 54 -
Rwork0.367 1011 -
obs-1210 88.24 %

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