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- PDB-2jlt: Crystal structure of an RNA kissing complex -

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Basic information

Entry
Database: PDB / ID: 2jlt
TitleCrystal structure of an RNA kissing complex
Components
  • R06
  • TAR
KeywordsRNA / KISSING COMPLEX
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9 Å
AuthorsDiPrimo, C. / Fribourg, S.
CitationJournal: Nucleic Acids Res. / Year: 2008
Title: Exploring Tar-RNA Aptamer Loop-Loop Interaction by X-Ray Crystallography, Uv Spectroscopy and Surface Plasmon Resonance.
Authors: Lebars, I. / Legrand, P. / Aime, A. / Pinaud, N. / Fribourg, S. / Di Primo, C.
History
DepositionSep 15, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 18, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Apr 19, 2017Group: Data collection
Revision 1.3Jul 12, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: R06
B: TAR


Theoretical massNumber of molelcules
Total (without water)11,0882
Polymers11,0882
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1020 Å2
ΔGint4 kcal/mol
Surface area7240 Å2
MethodPQS
Unit cell
Length a, b, c (Å)85.000, 85.000, 85.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213

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Components

#1: RNA chain R06 / 5'-R(*GP*GP*5BUP*CP*GP*GP*UP*CP*CP*CP*AP *GP*AP*CP*GP*AP*CP*C)-3'


Mass: 5841.395 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ESCHERICHIA COLI (E. coli)
#2: RNA chain TAR / 5'-R(*GP*GP*AP*GP*CP*CP*UP*GP*GP*GP *AP*GP*CP*5BUP*CP*C)-3'


Mass: 5247.030 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ESCHERICHIA COLI (E. coli)

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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: 2.28 Å3/Da / Density % sol: 46 % / Description: NONE
Crystal growpH: 4.6 / Details: NA CITRATE 100MM, MPD 35%, pH 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.91
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 3, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 2.9→20 Å / Num. obs: 10330 / % possible obs: 98.9 % / Observed criterion σ(I): 2 / Redundancy: 6.43 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 18.66
Reflection shellResolution: 2.9→3.07 Å / Redundancy: 6.09 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 5.45 / % possible all: 96.6

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Processing

Software
NameVersionClassification
REFMAC5.5.0054refinement
XDSdata reduction
SCALAdata scaling
autoSHARPphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.9→60.08 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.921 / SU B: 25.93 / SU ML: 0.205 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.37 / ESU R Free: 0.269 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES ARE RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.227 216 4.6 %RANDOM
Rwork0.187 ---
obs0.189 4510 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.54 Å2
Refinement stepCycle: LAST / Resolution: 2.9→60.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 725 0 0 725
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.021809
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.46831260
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0480.2168
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02357
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.7513809
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.1684.51260
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.98 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.294 6
Rwork0.333 344
Refinement TLS params.Method: refined / Origin x: -1.709 Å / Origin y: -23.895 Å / Origin z: -24.352 Å
111213212223313233
T0.4363 Å20.1034 Å2-0.0262 Å2-0.5888 Å2-0.0528 Å2--0.3942 Å2
L2.5556 °2-2.957 °20.415 °2-5.8291 °2-0.4585 °2--0.1108 °2
S0.024 Å °0.6143 Å °0.0444 Å °-0.4119 Å °0.1042 Å °-0.2838 Å °0.0117 Å °0.0951 Å °-0.1282 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 18
2X-RAY DIFFRACTION1B1 - 16

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