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- PDB-3loa: Crystal Structure Analysis of the RNA construct with two adjacent... -

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Basic information

Entry
Database: PDB / ID: 3loa
TitleCrystal Structure Analysis of the RNA construct with two adjacent ligand binding sites of helix h44 in 16S ribosomal RNA
Components
  • 5'-R(*CP*CP*GP*CP*GP*CP*CP*CP*GP*(5BU)P*CP*AP*CP*AP*CP*CP*AP*CP*CP*CP*G)-3'
  • 5'-R(*GP*GP*GP*(5BU)P*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*UP*AP*AP*CP*GP*CP*GP*GP*C)-3'
KeywordsRNA / A-site / Hygromycin B binding site / aminoglycoside
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.299 Å
AuthorsDibrov, S.
CitationJournal: Nucleic Acids Res. / Year: 2010
Title: A model for the study of ligand binding to the ribosomal RNA helix h44.
Authors: Dibrov, S.M. / Parsons, J. / Hermann, T.
History
DepositionFeb 3, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 4, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.name ..._software.classification / _software.name / _software.version / _struct_conn.pdbx_leaving_atom_flag
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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: 5'-R(*CP*CP*GP*CP*GP*CP*CP*CP*GP*(5BU)P*CP*AP*CP*AP*CP*CP*AP*CP*CP*CP*G)-3'
B: 5'-R(*GP*GP*GP*(5BU)P*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*UP*AP*AP*CP*GP*CP*GP*GP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5347
Polymers14,2692
Non-polymers2655
Water52229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3940 Å2
ΔGint-41 kcal/mol
Surface area7850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.455, 57.455, 58.433
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64
Components on special symmetry positions
IDModelComponents
11B-27-

HOH

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Components

#1: RNA chain 5'-R(*CP*CP*GP*CP*GP*CP*CP*CP*GP*(5BU)P*CP*AP*CP*AP*CP*CP*AP*CP*CP*CP*G)-3'


Mass: 6675.907 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: 16S rRNA helix 44
#2: RNA chain 5'-R(*GP*GP*GP*(5BU)P*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*UP*AP*AP*CP*GP*CP*GP*GP*C)-3'


Mass: 7593.416 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: 16S rRNA helix 44
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 29 / 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: 1.95 Å3/Da / Density % sol: 36.96 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1 mM magnesium chloride, 1.95 M ammonium sulfate, 50 mM sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.919411 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 29, 2008
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.919411 Å / Relative weight: 1
ReflectionResolution: 2.3→28.7 Å / Num. obs: 4941 / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 12.5 % / Biso Wilson estimate: 61.5 Å2 / Net I/σ(I): 36.22
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 12.2 % / Mean I/σ(I) obs: 5.31 / Num. unique all: 946

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine)refinement
CNSrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: SAD / Resolution: 2.299→28.728 Å / SU ML: 0.42 / Isotropic thermal model: Isotropic / σ(F): 1.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2305 439 4.61 %RANDOM
Rwork0.1906 ---
obs0.1923 4921 99.06 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.477 Å2 / ksol: 0.323 e/Å3
Refinement stepCycle: LAST / Resolution: 2.299→28.728 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 935 13 29 977
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071051
X-RAY DIFFRACTIONf_angle_d1.4371636
X-RAY DIFFRACTIONf_dihedral_angle_d17.112436
X-RAY DIFFRACTIONf_chiral_restr0.054216
X-RAY DIFFRACTIONf_plane_restr0.00444
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2986-2.6310.31411650.28733005X-RAY DIFFRACTION98.84
2.631-3.3140.25851470.24323040X-RAY DIFFRACTION99.56
3.314-28.72970.19631270.15333034X-RAY DIFFRACTION98.78
Refinement TLS params.Method: refined / Origin x: 26.4843 Å / Origin y: 13.8319 Å / Origin z: 18.7602 Å
111213212223313233
T0.3681 Å2-0.0502 Å2-0.0213 Å2-0.6772 Å20.0676 Å2--0.4733 Å2
L0.7434 °2-0.0392 °20.5575 °2--0.6248 °20.3597 °2--0.0082 °2
S-0.1369 Å °-0.0583 Å °0.1621 Å °0.1125 Å °0.1127 Å °-0.0008 Å °0.0497 Å °-0.0962 Å °0.0019 Å °
Refinement TLS groupSelection details: all

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