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- PDB-4erl: Crystal structure of the lysine riboswitch bound to a lysine-glyc... -

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Basic information

Entry
Database: PDB / ID: 4erl
TitleCrystal structure of the lysine riboswitch bound to a lysine-glycine dipeptide
ComponentsLysine riboswitch RNA
KeywordsTRANSCRIPTION / Riboswitch aptamer domain / regulatory mRNA
Function / homologyGLYCINE / LYSINE / RNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciesThermotoga Maritima (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsGarst, A.D. / Porter, E. / Batey, R.T.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: Insights into the regulatory landscape of the lysine riboswitch.
Authors: Garst, A.D. / Porter, E.B. / Batey, R.T.
History
DepositionApr 20, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 18, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2012Group: Database references
Revision 1.2Sep 13, 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: Lysine riboswitch RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6883
Polymers52,4651
Non-polymers2222
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)119.878, 119.878, 58.743
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 Lysine riboswitch RNA


Mass: 52465.289 Da / Num. of mol.: 1 / Fragment: Lysine riboswitch aptamer domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga Maritima (bacteria) / Gene: asd
#2: Chemical ChemComp-LYS / LYSINE


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N2O2
#3: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 73.52 %
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 10 mM Na-HEPES pH 7.0, 2 M Li2SO4, and 5 mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 303K

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 12, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→19.62 Å / Num. all: 18847 / % possible obs: 97.8 % / Observed criterion σ(F): 1.97 / Observed criterion σ(I): 2 / Redundancy: 1.92 % / Biso Wilson estimate: 47.24 Å2 / Rmerge(I) obs: 0.113 / Rsym value: 0.113 / Net I/σ(I): 5.1
Reflection shellResolution: 3→3.11 Å / Redundancy: 1.93 % / Rmerge(I) obs: 0.321 / Mean I/σ(I) obs: 1.9 / Num. unique all: 1853 / Rsym value: 0.321 / % possible all: 96.5

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHENIX(phenix.refine: 1.7.3_928)refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3D0U)

3d0u


Resolution: 3→19.62 Å / SU ML: 0.43 / σ(F): 1.97 / Phase error: 26.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2338 965 5.16 %RANDOM
Rwork0.1953 ---
obs0.1974 18687 99.16 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 11.901 Å2 / ksol: 0.254 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.5935 Å20 Å20 Å2
2--2.5935 Å2-0 Å2
3---10.4317 Å2
Refine analyzeLuzzati d res low obs: 0.43 Å
Refinement stepCycle: LAST / Resolution: 3→19.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 3479 14 10 3503
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073910
X-RAY DIFFRACTIONf_angle_d0.9336101
X-RAY DIFFRACTIONf_dihedral_angle_d13.8481941
X-RAY DIFFRACTIONf_chiral_restr0.06805
X-RAY DIFFRACTIONf_plane_restr0.008162
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.15820.37251360.31912537X-RAY DIFFRACTION98
3.1582-3.35510.2911180.26342508X-RAY DIFFRACTION99
3.3551-3.61270.30931590.2332532X-RAY DIFFRACTION99
3.6127-3.97350.26021300.20792517X-RAY DIFFRACTION99
3.9735-4.54230.22281290.17422564X-RAY DIFFRACTION100
4.5423-5.69940.18991580.15762512X-RAY DIFFRACTION100
5.6994-19.62010.16431350.14052552X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -23.1393 Å / Origin y: 45.4269 Å / Origin z: 1264.8736 Å
111213212223313233
T0.0362 Å2-0.0029 Å2-0.1095 Å2-0.0814 Å20.0996 Å2--0.073 Å2
L0.545 °2-0.1584 °20.2187 °2-0.2064 °2-0.1208 °2--0.3659 °2
S0.0491 Å °-0.044 Å °-0.0035 Å °0.0085 Å °0.0701 Å °0.0342 Å °-0.0629 Å °0.1073 Å °0.0133 Å °
Refinement TLS groupSelection details: all

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