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- PDB-3d0x: Crystal Structure of the unbound lysine riboswitch -

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Basic information

Entry
Database: PDB / ID: 3d0x
TitleCrystal Structure of the unbound lysine riboswitch
ComponentsRNA (161-MER)
KeywordsRNA / riboswitch
Function / homologyRNA / RNA (> 10) / RNA (> 100)
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.95 Å
AuthorsBatey, R.T. / Garst, A.D. / Heroux, A. / Rambo, R.P.
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 1.2Feb 26, 2020Group: Data collection / Category: reflns / reflns_shell
Item: _reflns.pdbx_Rmerge_I_obs / _reflns_shell.Rmerge_I_obs
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA (161-MER)


Theoretical massNumber of molelcules
Total (without water)52,4651
Polymers52,4651
Non-polymers00
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)120.193, 120.193, 58.248
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: RNA chain RNA (161-MER)


Mass: 52465.289 Da / Num. of mol.: 1 / Fragment: ligand binding domain / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 4.63 Å3/Da / Density % sol: 73.43 %
Crystal growDetails: LITHIUM SULFATE, MAGNESIUM CHLORIDE, IRIDIUM HEXAMMINE, SODIUM HEPES
Components of the solutions
IDNameCrystal-IDSol-ID
1LITHIUM SULFATE11
2MAGNESIUM CHLORIDE11
3IRIDIUM HEXAMMINE11
4SODIUM HEPES11
5LITHIUM SULFATE12
6MAGNESIUM CHLORIDE12
7IRIDIUM HEXAMMINE12
8SODIUM HEPES12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 26, 2008
RadiationMonochromator: Ni filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.95→19.7 Å / Num. obs: 19610 / % possible obs: 99.4 % / Redundancy: 3.62 % / Biso Wilson estimate: 55.12 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 10.2
Reflection shellResolution: 2.95→3.06 Å / Redundancy: 3.63 % / Rmerge(I) obs: 0.355 / Mean I/σ(I) obs: 3.4 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.95 Å17.11 Å
Translation2.95 Å17.11 Å

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Processing

Software
NameVersionClassificationNB
d*TREKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.005data extraction
CrystalCleardata collection
d*TREKdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3D0U without lysine

3d0u


Resolution: 2.95→17.112 Å / SU ML: 0.42 / Phase error: 23.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2203 1999 10.19 %
Rwork0.1872 --
obs0.1907 19610 99.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 8.987 Å2 / ksol: 0.208 e/Å3
Displacement parametersBiso mean: 54.92 Å2
Baniso -1Baniso -2Baniso -3
1--7.97 Å2-0 Å20 Å2
2---7.97 Å2-0 Å2
3---15.941 Å2
Refinement stepCycle: LAST / Resolution: 2.95→17.112 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 3479 0 60 3539
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043898
X-RAY DIFFRACTIONf_angle_d1.056088
X-RAY DIFFRACTIONf_dihedral_angle_d19.3321607
X-RAY DIFFRACTIONf_chiral_restr0.069804
X-RAY DIFFRACTIONf_plane_restr0.002161
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.95-3.0230.3831430.35112731416100
3.023-3.1050.361480.31512581406100
3.105-3.1960.3251420.27312571399100
3.196-3.2980.2471480.24512511399100
3.298-3.4150.31450.22912791424100
3.415-3.5510.2551400.21812601400100
3.551-3.7110.2191400.19612721412100
3.711-3.9040.2471360.18812771413100
3.904-4.1450.251480.17612621410100
4.145-4.460.221370.1631247138499
4.46-4.8990.1811400.15812631403100
4.899-5.5870.1551370.1312651402100
5.587-6.9590.1651460.1331243138999
6.959-17.1130.1441490.1291204135396

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