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- PDB-1g1x: STRUCTURE OF RIBOSOMAL PROTEINS S15, S6, S18, AND 16S RIBOSOMAL RNA -

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Basic information

Entry
Database: PDB / ID: 1g1x
TitleSTRUCTURE OF RIBOSOMAL PROTEINS S15, S6, S18, AND 16S RIBOSOMAL RNA
Components
  • (16S RIBOSOMAL RNA) x 2
  • 30S RIBOSOMAL PROTEIN S15
  • 30S RIBOSOMAL PROTEIN S18
  • 30S RIBOSOMAL PROTEIN S6
KeywordsRIBOSOME / ribosomal proteins S15 / S6 / S18 / S30 ribosomal subunit / RNA
Function / homology
Function and homology information


rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / cytoplasm
Similarity search - Function
Ribosomal protein S18 / 30s Ribosomal Protein S18 / Ribosomal protein S6/Translation elongation factor EF1B / S15/NS1, RNA-binding / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / Ribosomal protein S15, bacterial-type ...Ribosomal protein S18 / 30s Ribosomal Protein S18 / Ribosomal protein S6/Translation elongation factor EF1B / S15/NS1, RNA-binding / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / Ribosomal protein S15, bacterial-type / Ribosomal protein S6 / Ribosomal protein S6 / Ribosomal protein S6 superfamily / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein S18 / Ribosomal protein S18 / Ribosomal protein S18 superfamily / Few Secondary Structures / Irregular / Ribosomal_S15 / Ribosomal protein S15 signature. / Ribosomal protein S15 / Ribosomal protein S15 / S15/NS1, RNA-binding / Helix Hairpins / Alpha-Beta Plaits / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein bS18
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.6 Å
AuthorsAgalarov, S.C. / Prasad, G.S. / Funke, P.M. / Stout, C.D. / Williamson, J.R.
CitationJournal: Science / Year: 2000
Title: Structure of the S15,S6,S18-rRNA complex: assembly of the 30S ribosome central domain.
Authors: Agalarov, S.C. / Sridhar Prasad, G. / Funke, P.M. / Stout, C.D. / Williamson, J.R.
History
DepositionOct 13, 2000Deposition site: RCSB / Processing site: RCSB
SupersessionOct 30, 2000ID: 1EKC
Revision 1.0Oct 30, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: 16S RIBOSOMAL RNA
E: 16S RIBOSOMAL RNA
I: 16S RIBOSOMAL RNA
J: 16S RIBOSOMAL RNA
A: 30S RIBOSOMAL PROTEIN S6
B: 30S RIBOSOMAL PROTEIN S15
C: 30S RIBOSOMAL PROTEIN S18
F: 30S RIBOSOMAL PROTEIN S6
G: 30S RIBOSOMAL PROTEIN S15
H: 30S RIBOSOMAL PROTEIN S18


Theoretical massNumber of molelcules
Total (without water)120,29310
Polymers120,29310
Non-polymers00
Water0
1
D: 16S RIBOSOMAL RNA
E: 16S RIBOSOMAL RNA
A: 30S RIBOSOMAL PROTEIN S6
B: 30S RIBOSOMAL PROTEIN S15
C: 30S RIBOSOMAL PROTEIN S18


Theoretical massNumber of molelcules
Total (without water)60,1475
Polymers60,1475
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
I: 16S RIBOSOMAL RNA
J: 16S RIBOSOMAL RNA
F: 30S RIBOSOMAL PROTEIN S6
G: 30S RIBOSOMAL PROTEIN S15
H: 30S RIBOSOMAL PROTEIN S18


Theoretical massNumber of molelcules
Total (without water)60,1475
Polymers60,1475
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)169.5, 169.5, 113.8
Angle α, β, γ (deg.)90.0, 90.0, 120.0
Int Tables number170
Cell settinghexagonal
Space group name H-MP65

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Components

#1: RNA chain 16S RIBOSOMAL RNA /


Mass: 13576.196 Da / Num. of mol.: 2 / Fragment: RESIDUES 582-675 / Source method: obtained synthetically
#2: RNA chain 16S RIBOSOMAL RNA /


Mass: 14102.433 Da / Num. of mol.: 2 / Fragment: RESIDUES 716-759 / Source method: obtained synthetically
#3: Protein 30S RIBOSOMAL PROTEIN S6 /


Mass: 11732.494 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: Q5SLP8
#4: Protein 30S RIBOSOMAL PROTEIN S15 /


Mass: 10491.223 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: Q5SJ76
#5: Protein 30S RIBOSOMAL PROTEIN S18 /


Mass: 10244.272 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: Q5SLQ0

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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: 3.4 Å3/Da / Density % sol: 75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.8 M (NH4)2SO4, 20 mM MgCl2, 50 mM Potassium Cacodylate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1MgCl211
2Potassium Cacodylate11
3(NH4)2SO411
4(NH4)2SO412
Crystal grow
*PLUS
pH: 6.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11.8 Mammonium sulfate1reservoir
220 mM1reservoirMgCl2
350 mMpotassium cacodylate1reservoir
41

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 26, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 57348 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 71.4 Å2 / Rmerge(I) obs: 0.051 / Rsym value: 0.279 / Net I/σ(I): 9.9
Reflection shellResolution: 2.6→2.69 Å / % possible obs: 99.9 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 1.7 / Rsym value: 0.279 / % possible all: 99.9
Reflection
*PLUS
Num. measured all: 264392

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Processing

Software
NameVersionClassification
MLPHAREphasing
X-PLORrefinement
MOSFLMdata reduction
CCP4(TRUNCATE)data scaling
RefinementMethod to determine structure: MIR / Resolution: 2.6→50 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.298 1289 2.2 %random
Rwork0.266 ---
obs-57348 99.9 %-
Displacement parametersBiso mean: 44.48 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.68 Å0.58 Å
Luzzati d res low-5 Å
Luzzati sigma a0.65 Å0.73 Å
Refinement stepCycle: LAST / Resolution: 2.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3897 3646 0 0 7543
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.023
X-RAY DIFFRACTIONx_angle_deg2.22
X-RAY DIFFRACTIONx_dihedral_angle_d19.45
X-RAY DIFFRACTIONx_improper_angle_d1.81
X-RAY DIFFRACTIONx_mcbond_it4.34
X-RAY DIFFRACTIONx_mcangle_it6.35
X-RAY DIFFRACTIONx_scbond_it5.58
X-RAY DIFFRACTIONx_scangle_it7.75
LS refinement shellResolution: 2.6→2.72 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.48 60 2.2 %
Rwork0.42 7071 -
obs--99.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 50 Å / σ(F): 0 / % reflection Rfree: 2.2 % / Rfactor obs: 0.266
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg19.45
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.81
LS refinement shell
*PLUS
Rfactor Rfree: 0.48 / % reflection Rfree: 2.2 % / Rfactor Rwork: 0.42

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