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- PDB-3dis: Crystallization of the Thermotoga maritima lysine riboswitch in f... -

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Basic information

Entry
Database: PDB / ID: 3dis
TitleCrystallization of the Thermotoga maritima lysine riboswitch in free form
ComponentsRNA (174-MER)
KeywordsRNA / free form / riboswitch
Function / homologyISOPROPYL ALCOHOL / RNA / RNA (> 10) / RNA (> 100)
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.1 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: 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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: RNA (174-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,94913
Polymers56,6361
Non-polymers31312
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.252, 78.624, 141.876
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#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
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2.67 Å3/Da / Density % sol: 53.96 %
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: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: May 12, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 3.1→20 Å / Num. all: 11469 / Num. obs: 10643 / % possible obs: 92.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Rmerge(I) obs: 0.197 / Net I/σ(I): 7.5
Reflection shellResolution: 3.1→3.2 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.499 / Mean I/σ(I) obs: 2.8 / Num. unique all: 1124 / % possible all: 89.5

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Processing

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

3dil


Resolution: 3.1→20 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.903 / SU B: 43.734 / SU ML: 0.347 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.451 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22764 516 4.9 %RANDOM
Rwork0.18773 ---
all0.1896 10917 --
obs0.1896 10098 92.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.715 Å2
Baniso -1Baniso -2Baniso -3
1--2.94 Å20 Å20 Å2
2---3.8 Å20 Å2
3---6.74 Å2
Refine analyzeLuzzati coordinate error obs: 0.347 Å
Refinement stepCycle: LAST / Resolution: 3.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 3752 14 6 3772
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0214202
X-RAY DIFFRACTIONr_angle_refined_deg1.22836560
X-RAY DIFFRACTIONr_chiral_restr0.0680.2869
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021834
X-RAY DIFFRACTIONr_nbd_refined0.1580.21666
X-RAY DIFFRACTIONr_nbtor_refined0.270.22608
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2137
X-RAY DIFFRACTIONr_metal_ion_refined0.040.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1640.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1840.212
X-RAY DIFFRACTIONr_mcbond_it0.0991.52
X-RAY DIFFRACTIONr_scbond_it0.47235054
X-RAY DIFFRACTIONr_scangle_it0.8194.56560
LS refinement shellResolution: 3.1→3.182 Å / Rfactor Rfree error: 0.451 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 30 -
Rwork0.275 668 -
obs-833 83.79 %
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)
10.94440.62630.87552.5579-1.9053.69510.0470.3282-0.3385-0.46070.06730.05240.266-0.3671-0.1143-0.13280.03060.0165-0.06-0.0128-0.118529.5161-1.755418.8782
20.8621-0.05050.28790.65490.17540.9694-0.10330.08970.3795-0.0637-0.00480.0698-0.4364-0.23490.10810.02960.06330.0335-0.04240.01130.05387.018747.10521.1044
30.95870.34080.31850.12710.06050.56740.11050.3365-0.1023-0.0045-0.07890.1392-0.13220.0104-0.0316-0.0610.02350.0233-0.0495-0.0266-0.0898.694627.208111.0468
43.0823-0.84130.51940.2435-0.24780.89860.25990.37550.2819-0.1161-0.1479-0.3993-0.2449-0.0153-0.112-0.05930.0221-0.0047-0.05430.0859-0.108129.790833.772715.0989
52.4821.1749-0.10340.67960.24550.7066-0.32280.0328-0.79540.41060.0395-0.1480.27110.12830.2833-0.06360.03770.01960.0720.01780.261650.39638.690315.6012
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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