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- PDB-3d0u: Crystal Structure of Lysine Riboswitch Bound to Lysine -

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Basic information

Entry
Database: PDB / ID: 3d0u
TitleCrystal Structure of Lysine Riboswitch Bound to Lysine
ComponentsLysine Riboswitch RNA
KeywordsRNA / RNA-ligand complex / riboswitch
Function / homologyIRIDIUM HEXAMMINE ION / LYSINE / RNA / RNA (> 10) / RNA (> 100)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsGarst, A.D. / Heroux, A. / Rambo, R.P. / Batey, R.T.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Crystal structure of the lysine riboswitch regulatory mRNA element.
Authors: Garst, A.D. / Heroux, A. / Rambo, R.P. / Batey, R.T.
History
DepositionMay 2, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Lysine Riboswitch RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4965
Polymers52,4651
Non-polymers1,0304
Water81145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)119.823, 119.823, 58.744
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32

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Components

#1: RNA chain Lysine Riboswitch RNA


Mass: 52465.289 Da / Num. of mol.: 1 / Fragment: Ligand binding domain / Source method: obtained synthetically / Details: sequence occurs naturally in Thermotoga Maritima
#2: Chemical ChemComp-IRI / IRIDIUM HEXAMMINE ION


Mass: 294.400 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: H18IrN6
#3: Chemical ChemComp-LYS / LYSINE / Lysine


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


Mass: 18.015 Da / Num. of mol.: 45 / 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: 4.64 Å3/Da / Density % sol: 73.5 %
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2 M Li2SO4, 5 mM MgCl2, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 303K
Components of the solutions
IDNameCrystal-IDSol-ID
1Li2SO411
2MgCl211
3Li2SO412
4MgCl212

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.105 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 28, 2008
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.105 Å / Relative weight: 1
ReflectionRedundancy: 5 % / Av σ(I) over netI: 13.5 / Number: 122605 / Rmerge(I) obs: 0.084 / Χ2: 2.35 / D res high: 2.7 Å / D res low: 40 Å / Num. obs: 24657 / % possible obs: 95.6
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.814099.110.0656.0035.2
4.625.8110010.0754.085.3
4.034.6210010.0762.7415.4
3.664.0310010.082.2255.5
3.43.6610010.0931.8435.5
3.23.410010.111.6325.5
3.043.210010.1421.2015.4
2.913.0499.910.2220.6725
2.82.9196.610.3480.4873.7
2.72.861.410.4030.4042.2
ReflectionResolution: 2.7→40 Å / Num. obs: 24657 / % possible obs: 95.6 % / Redundancy: 5 % / Rmerge(I) obs: 0.084 / Χ2: 2.353 / Net I/σ(I): 13.5
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.403 / Num. unique all: 1601 / Χ2: 0.404 / % possible all: 61.4

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
PHENIXrefinement
PDB_EXTRACT3.005data extraction
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.8→32.619 Å / FOM work R set: 0.862 / σ(F): 0.41 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.209 1889 8.34 %
Rwork0.182 --
obs0.184 22659 97.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 8.453 Å2 / ksol: 0.208 e/Å3
Displacement parametersBiso max: 16.66 Å2 / Biso mean: 54.61 Å2 / Biso min: 549.57 Å2
Baniso -1Baniso -2Baniso -3
1--7.9203 Å2-0 Å20 Å2
2---7.9203 Å2-0 Å2
3---15.8407 Å2
Refinement stepCycle: LAST / Resolution: 2.8→32.619 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 3479 31 45 3555
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053909
X-RAY DIFFRACTIONf_angle_d1.0876106
X-RAY DIFFRACTIONf_chiral_restr0.07802
X-RAY DIFFRACTIONf_plane_restr0.002161
X-RAY DIFFRACTIONf_dihedral_angle_d20.481616
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8-2.8760.3461180.3191379149786
2.876-2.960.3111380.3061535167393
2.96-3.0560.291540.2631585173998
3.056-3.1650.2871520.2511618177099
3.165-3.2920.2491450.2181622176799
3.292-3.4410.2141490.2041635178499
3.441-3.6220.1961540.1841613176799
3.622-3.8490.1931470.1711623177099
3.849-4.1460.1841380.1621642178099
4.146-4.5620.1821430.14216271770100
4.562-5.220.1511510.13716391790100
5.22-6.5670.1691500.12616311781100
6.567-32.6210.1441500.1291621177199

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