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- PDB-1f7y: THE CRYSTAL STRUCTURE OF TWO UUCG LOOPS HIGHLIGHTS THE ROLE PLAYE... -

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Basic information

Entry
Database: PDB / ID: 1f7y
TitleTHE CRYSTAL STRUCTURE OF TWO UUCG LOOPS HIGHLIGHTS THE ROLE PLAYED BY 2'-HYDROXYL GROUPS IN ITS UNUSUAL STABILITY
Components
  • 16S RIBOSOMAL RNA FRAGMENT
  • 30S RIBOSOMAL PROTEIN S15
KeywordsRIBOSOME / UUCG / TETRALOOP / RNA
Function / homology
Function and homology information


rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / cytoplasm
Similarity search - Function
S15/NS1, RNA-binding / Ribosomal protein S15, bacterial-type / Ribosomal_S15 / Ribosomal protein S15 signature. / Ribosomal protein S15 / Ribosomal protein S15 / S15/NS1, RNA-binding / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / RNA / RNA (> 10) / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS15
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 Å
AuthorsEnnifar, E. / Nikouline, A. / Serganov, A. / Tishchenko, S. / Nevskaya, N. / Garber, M. / Ehresmann, B. / Ehresmann, C. / Nikonov, S. / Dumas, P.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: The crystal structure of UUCG tetraloop.
Authors: Ennifar, E. / Nikulin, A. / Tishchenko, S. / Serganov, A. / Nevskaya, N. / Garber, M. / Ehresmann, B. / Ehresmann, C. / Nikonov, S. / Dumas, P.
History
DepositionJun 28, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 28, 2011Group: Advisory
Revision 1.4Nov 3, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / diffrn_source ...database_2 / diffrn_source / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_ref_seq_dif.details / _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
B: 16S RIBOSOMAL RNA FRAGMENT
A: 30S RIBOSOMAL PROTEIN S15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,61314
Polymers29,3092
Non-polymers30412
Water48627
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)128.800, 128.800, 65.100
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Cell settinghexagonal
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11B-1012-

HOH

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Components

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RNA chain / Protein , 2 types, 2 molecules BA

#1: RNA chain 16S RIBOSOMAL RNA FRAGMENT


Mass: 18464.963 Da / Num. of mol.: 1 / Fragment: 57 RESIDUES / Source method: obtained synthetically / Details: SEQUENCE OCCURS NATURALLY IN THERMUS THERMOPHILUS
#2: Protein 30S RIBOSOMAL PROTEIN S15 /


Mass: 10844.145 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P80378, UniProt: Q5SJ76*PLUS

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Non-polymers , 4 types, 39 molecules

#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 2.66 Å3/Da / Density % sol: 53.74 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 1 M (NH4)2SO4, 100 MM SODIUM CACODYLATE, 30 MM KCL, 1.5 MM MGCL2, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Components of the solutions
IDNameCrystal-IDSol-ID
1SODIUM CACODYLATE11
2KCL11
3MGCL211
4(NH4)2SO411
5KCL12
6MGCL212
7(NH4)2SO412
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
16 mg/mlRNA1drop
23 mg/mlS151drop
31.0 Mammonium sulfate1reservoir
41.5 mM1reservoirMgCl2
550 mM1reservoirKCl
650 mMsodium cacodylate1reservoirpH6.2
71

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.94654
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 18, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.94654 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. obs: 8164 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.1 % / Rmerge(I) obs: 0.038
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.209 / % possible all: 99.5
Reflection
*PLUS
Num. obs: 14823
Reflection shell
*PLUS
% possible obs: 99.5 % / Redundancy: 6.3 %

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Processing

Software
NameVersionClassification
SHARPphasing
CNS0.4refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.8→8 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 578374.93 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.289 640 8.3 %RANDOM
Rwork0.222 ---
obs0.222 7679 98.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 85.64 Å2 / ksol: 0.42 e/Å3
Displacement parametersBiso mean: 61.5 Å2
Baniso -1Baniso -2Baniso -3
1--5.97 Å22.6 Å20 Å2
2---5.97 Å20 Å2
3---11.95 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.5 Å0.36 Å
Luzzati d res low-8 Å
Luzzati sigma a0.37 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms721 1221 12 27 1981
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d16.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.97
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it4.341.5
X-RAY DIFFRACTIONc_mcangle_it6.732
X-RAY DIFFRACTIONc_scbond_it6.692
X-RAY DIFFRACTIONc_scangle_it9.172.5
LS refinement shellResolution: 2.8→2.97 Å / Rfactor Rfree error: 0.044 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.442 101 8.6 %
Rwork0.346 1078 -
obs--92.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1LUC.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION2WATER_REP.PARAWATER.TOP
X-RAY DIFFRACTION3ION2.PARAMION.TOP
X-RAY DIFFRACTION4PROTEIN_REP.PA
Software
*PLUS
Name: CNS / Version: 0.4 / Classification: refinement
Refinement
*PLUS
σ(F): 2 / % reflection Rfree: 8.3 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 61.5 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg16.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.97
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.442 / % reflection Rfree: 8.6 % / Rfactor Rwork: 0.346

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