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

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Basic information

Entry
Database: PDB / ID: 3diy
TitleCrystallization of the Thermotoga maritima lysine riboswitch bound to lysine, Mn2+ soak
ComponentsRNA (174-MER)
KeywordsRNA / riboswitch / lysine
Function / homology: / LYSINE / : / RNA / RNA (> 10) / RNA (> 100)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.71 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 21, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 30, 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_label_atom_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 / _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
A: RNA (174-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,19613
Polymers56,7161
Non-polymers48012
Water66737
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.193, 78.662, 140.522
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: 56715.578 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, 49 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.: 8 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#5: Chemical ChemComp-LYS / LYSINE


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N2O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 2.64 Å3/Da / Density % sol: 53.42 %
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-C / Wavelength: 1.24 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 17, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.24 Å / Relative weight: 1
ReflectionResolution: 2.7→20 Å / Num. all: 16969 / Num. obs: 16392 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 21.8
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.588 / Mean I/σ(I) obs: 2.8 / Num. unique all: 1658 / % possible all: 95.9

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Processing

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

3dil


Resolution: 2.71→20 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.916 / SU B: 24.836 / SU ML: 0.233 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: tls / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 2.039 / ESU R Free: 0.327 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23671 822 5 %RANDOM
Rwork0.18872 ---
all0.19099 16107 --
obs0.19099 15510 96.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.039 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20 Å20 Å2
2---1.91 Å20 Å2
3---1.71 Å2
Refine analyzeLuzzati coordinate error obs: 0.233 Å
Refinement stepCycle: LAST / Resolution: 2.71→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 3756 21 37 3814
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0214213
X-RAY DIFFRACTIONr_angle_refined_deg1.2392.9996572
X-RAY DIFFRACTIONr_dihedral_angle_3_deg8.221154
X-RAY DIFFRACTIONr_chiral_restr0.0510.2870
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021838
X-RAY DIFFRACTIONr_nbd_refined0.1550.21455
X-RAY DIFFRACTIONr_nbtor_refined0.2650.22586
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2137
X-RAY DIFFRACTIONr_metal_ion_refined0.1470.24
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1260.233
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1710.28
X-RAY DIFFRACTIONr_mcbond_it0.1231.55
X-RAY DIFFRACTIONr_mcangle_it0.31227
X-RAY DIFFRACTIONr_scbond_it0.66634450
X-RAY DIFFRACTIONr_scangle_it1.0454.56565
LS refinement shellResolution: 2.71→2.776 Å / Rfactor Rfree error: 0.327 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.545 69 -
Rwork0.414 1057 -
obs-1126 93.44 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.80671.4331.40914.921-0.68115.04850.12330.2358-0.1968-0.4825-0.0571-0.2060.7162-0.0995-0.06620.09770.06340.0204-0.0557-0.00290.002329.276-1.92218.527
21.36250.35230.79930.30260.61351.7578-0.4022-0.0440.6841-0.0269-0.01750.0235-0.6996-0.41380.41970.24060.1548-0.03240.016-0.00870.22276.77747.13721.337
33.0855-1.70651.14351.3328-0.83460.69950.08020.1332-0.15140.0269-0.02890.2007-0.0810.0726-0.0513-0.01480.059-0.0008-0.0015-0.01080.02238.40727.17110.831
44.7922-2.23920.89162.7999-0.06861.63730.11510.48440.3956-0.0912-0.2431-0.3034-0.22980.01020.1279-0.02490.0450.0172-0.06110.057-0.021229.65633.76214.846
58.66591.9908-2.4292.17081.04292.5875-0.3029-0.1971-1.08540.2895-0.1811-0.54310.48030.34670.4840.04640.08920.00910.02020.13620.219650.2118.62115.063
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 111 - 11
2X-RAY DIFFRACTION1AA163 - 174163 - 174
3X-RAY DIFFRACTION2AA12 - 7912 - 79
4X-RAY DIFFRACTION3AA80 - 11380 - 113
5X-RAY DIFFRACTION4AA114 - 140114 - 140
6X-RAY DIFFRACTION5AA141 - 162141 - 162

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