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- PDB-4erj: Crystal structure of the lysine riboswitch bound to a 6-aminocapr... -

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Basic information

Entry
Database: PDB / ID: 4erj
TitleCrystal structure of the lysine riboswitch bound to a 6-aminocaproic acid
ComponentsLysine riboswitch RNA
KeywordsTRANSCRIPTION / Riboswitch aptamer domain / regulatory mRNA / TRANSLATION
Function / homology6-AMINOHEXANOIC ACID / 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 1.2Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.3Sep 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_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
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lysine riboswitch RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,5962
Polymers52,4651
Non-polymers1311
Water362
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)119.655, 119.655, 58.698
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-ACA / 6-AMINOHEXANOIC ACID / AMINOCAPROIC ACID


Type: peptide linking / Mass: 131.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 4.62 Å3/Da / Density % sol: 73.4 %
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: Jul 23, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→59.83 Å / Num. all: 18821 / Num. obs: 18384 / % possible obs: 97.7 % / Observed criterion σ(I): 2 / Redundancy: 1.59 % / Biso Wilson estimate: 48.31 Å2 / Rmerge(I) obs: 0.098 / Rsym value: 0.098 / Net I/σ(I): 5.4
Reflection shellResolution: 3→3.11 Å / Redundancy: 1.58 % / Rmerge(I) obs: 0.338 / Mean I/σ(I) obs: 1.7 / Num. unique all: 18384 / Rsym value: 0.338 / % possible all: 99.9

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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 3D0X

3d0x


Resolution: 3→26.652 Å / SU ML: 0.33 / σ(F): 0.03 / σ(I): 2 / Phase error: 23.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2232 1735 9.85 %RANDOM
Rwork0.2074 ---
obs0.209 17611 93.68 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 13.948 Å2 / ksol: 0.261 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.1643 Å20 Å20 Å2
2---4.1643 Å2-0 Å2
3---8.3287 Å2
Refinement stepCycle: LAST / Resolution: 3→26.652 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 3479 9 2 3490
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073905
X-RAY DIFFRACTIONf_angle_d0.9146094
X-RAY DIFFRACTIONf_dihedral_angle_d13.1631935
X-RAY DIFFRACTIONf_chiral_restr0.065805
X-RAY DIFFRACTIONf_plane_restr0.007162
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.08850.35611380.36611290X-RAY DIFFRACTION90
3.0885-3.1880.34041390.31871303X-RAY DIFFRACTION94
3.188-3.30170.30781420.2811322X-RAY DIFFRACTION94
3.3017-3.43370.26911450.26711337X-RAY DIFFRACTION93
3.4337-3.58960.2451480.24781313X-RAY DIFFRACTION93
3.5896-3.77840.25461470.21441312X-RAY DIFFRACTION94
3.7784-4.01430.22481390.20241351X-RAY DIFFRACTION96
4.0143-4.32310.22711570.19521349X-RAY DIFFRACTION95
4.3231-4.75590.20751560.18271340X-RAY DIFFRACTION95
4.7559-5.4390.17341400.15181352X-RAY DIFFRACTION96
5.439-6.83340.16181510.15441320X-RAY DIFFRACTION95
6.8334-26.65340.14931330.14611287X-RAY DIFFRACTION90

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