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- PDB-1dk1: DETAILED VIEW OF A KEY ELEMENT OF THE RIBOSOME ASSEMBLY: CRYSTAL ... -

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Basic information

Entry
Database: PDB / ID: 1dk1
TitleDETAILED VIEW OF A KEY ELEMENT OF THE RIBOSOME ASSEMBLY: CRYSTAL STRUCTURE OF THE S15-RRNA COMPLEX
Components
  • 30S RIBOSOMAL PROTEIN S15
  • RRNA FRAGMENT
KeywordsRIBOSOME / S15 / PROTEIN / RNA
Function / homology
Function and homology information


rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / 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
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 Å
AuthorsNikulin, A. / Serganov, A. / Ennifar, E. / Tischenko, S. / Nevskaya, N.
CitationJournal: Nat.Struct.Biol. / Year: 2000
Title: Crystal structure of the S15-rRNA complex.
Authors: Nikulin, A. / Serganov, A. / Ennifar, E. / Tishchenko, S. / Nevskaya, N. / Shepard, W. / Portier, C. / Garber, M. / Ehresmann, B. / Ehresmann, C. / Nikonov, S. / Dumas, P.
History
DepositionDec 6, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 2, 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 1.4Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5Nov 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: RRNA FRAGMENT
A: 30S RIBOSOMAL PROTEIN S15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,26714
Polymers28,9642
Non-polymers30412
Water45025
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-301-

HOH

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Components

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RNA chain / Protein , 2 types, 2 molecules BA

#1: RNA chain RRNA FRAGMENT


Mass: 18464.963 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)
#2: Protein 30S RIBOSOMAL PROTEIN S15 /


Mass: 10498.702 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-87 / Mutation: ILE11MSE, ALA79MSE
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P80378

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Non-polymers , 4 types, 37 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.: 25 / 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: 2.69 Å3/Da / Density % sol: 54.29 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 100MM SODIUM CACODYLATE, 30 MM KCL, 1M (NH4)2SO4, 1.5 MM MGCL2, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 22K
Components of the solutions
IDNameCrystal-IDSol-ID
1SODIUM CACODYLATE11
2KCL11
3(NH4)2SO411
4MGCL211
5KCL12
6(NH4)2SO412
7MGCL212
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion / Details: drop:reservoir in a 3:2 volume ratio
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
16 mg/mlRNA1drop
23 mg/mlS151drop
31.0 Mammonium sulfate1reservoir
41.5 mM1reservoirMgCl2
550 mM1reservoirKCl
650 mMsodium cacodylate1reservoir
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 shell
*PLUS
% possible obs: 99.5 %

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Processing

Software
NameClassification
SHARPphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.8→8 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.291 640 8.3 %RANDOM
Rwork0.213 ---
obs0.213 7679 98.1 %-
all-8164 --
Refinement stepCycle: LAST / Resolution: 2.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms722 1221 12 25 1980
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
σ(F): 2 / % reflection Rfree: 8.3 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.4

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