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- PDB-1dv4: PARTIAL STRUCTURE OF 16S RNA OF THE SMALL RIBOSOMAL SUBUNIT FROM ... -

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Basic information

Entry
Database: PDB / ID: 1dv4
TitlePARTIAL STRUCTURE OF 16S RNA OF THE SMALL RIBOSOMAL SUBUNIT FROM THERMUS THERMOPHILUS
Components
  • 16S RIBOSOMAL RNA
  • RIBOSOMAL PROTEIN S5
  • RIBOSOMAL PROTEIN S7
KeywordsRIBOSOME / RIBOSOMES / 30S / THERMUS THERMOPHILUS / 16S RNA
Function / homology
Function and homology information


small ribosomal subunit / tRNA binding / rRNA binding / structural constituent of ribosome / translation / response to antibiotic / cytoplasm
Similarity search - Function
Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S5, bacterial-type / Ribosomal protein S7, conserved site / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S5 signature. / Ribosomal protein S5 / Ribosomal protein S5, N-terminal / Ribosomal protein S7 signature. / S5 double stranded RNA-binding domain profile. / Ribosomal protein S5, C-terminal ...Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S5, bacterial-type / Ribosomal protein S7, conserved site / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S5 signature. / Ribosomal protein S5 / Ribosomal protein S5, N-terminal / Ribosomal protein S7 signature. / S5 double stranded RNA-binding domain profile. / Ribosomal protein S5, C-terminal / Ribosomal protein S5, N-terminal domain / Ribosomal protein S5, C-terminal domain / Ribosomal protein S5/S7 / Ribosomal protein S7 domain / Ribosomal protein S7 domain superfamily / Ribosomal protein S7p/S5e / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
OCTADECATUNGSTENYL DIPHOSPHATE / RNA / RNA (> 10) / RNA (> 100) / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein uS7
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
Geobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 4.5 Å
AuthorsTocilj, A. / Schlunzen, F. / Janell, D. / Gluhmann, M. / Hansen, H. / Harms, J. / Bashan, A. / Bartels, H. / Agmon, I. / Franceschi, F. / Yonath, A.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 1999
Title: The small ribosomal subunit from Thermus thermophilus at 4.5 A resolution: pattern fittings and the identification of a functional site.
Authors: Tocilj, A. / Schlunzen, F. / Janell, D. / Gluhmann, M. / Hansen, H.A. / Harms, J. / Bashan, A. / Bartels, H. / Agmon, I. / Franceschi, F. / Yonath, A.
#1: Journal: Nature / Year: 1992
Title: The structure of ribosomal protein-S5 reveals sites of interaction with 16S ribosomal-RNA
Authors: Ramakrishnan, V. / White, S.
#2: Journal: Structure / Year: 1997
Title: The structure of ribosomal protein S7 at 1.9 angstrom resolution reveals a beta-hairpin motif that binds double-stranded nucleic acids
Authors: Wimberly, B.T. / White, S. / Ramakrishnan, V.
#3: Journal: Acta Crystallogr. / Year: 1953
Title: The structure of the 9(18)-heteropoly anion in potassium 9(18)-tungstophosphate, K6(P2W18O62).14H2O
Authors: Dawson, B.
History
DepositionJan 19, 2000Deposition site: RCSB / Processing site: RCSB
SupersessionFeb 2, 2000ID: 1C59
Revision 1.0Feb 2, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 2.0Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Polymer sequence
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / entity_poly / 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 / _entity_poly.pdbx_seq_one_letter_code / _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: 16S RIBOSOMAL RNA
E: RIBOSOMAL PROTEIN S5
G: RIBOSOMAL PROTEIN S7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,8884
Polymers101,5253
Non-polymers4,3631
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)407.100, 407.100, 176.008
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number92
Cell settingtetragonal
Space group name H-MP41212

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Components

#1: RNA chain 16S RIBOSOMAL RNA /


Mass: 70941.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria)
#2: Protein RIBOSOMAL PROTEIN S5 / / BS5 / Coordinate model: Cα atoms only


Mass: 15240.724 Da / Num. of mol.: 1 / Fragment: RESIDUES 4-148 / Source method: isolated from a natural source / Source: (natural) Geobacillus stearothermophilus (bacteria) / References: UniProt: P02357
#3: Protein RIBOSOMAL PROTEIN S7 / / Coordinate model: Cα atoms only


Mass: 15342.846 Da / Num. of mol.: 1 / Fragment: RESIDUES 12-146 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P17291
#4: Chemical ChemComp-WO2 / OCTADECATUNGSTENYL DIPHOSPHATE


Mass: 4363.030 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O62P2W18

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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

CrystalDescription: diffraction data were collected during years 1987-2000.
Crystal grow
*PLUS
Method: other / Details: Yonath, A., (1988) J. Mol. Biol., 203, 831.

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Data collection

Diffraction
IDCrystal-ID
11
21
31
41
51
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONEMBL/DESY, HAMBURG BW7B10.850, 1.300
SYNCHROTRONMPG/DESY, HAMBURG BW620.850, 1.300
SYNCHROTRONCHESS F130.850, 1.300
SYNCHROTRONAPS 19-ID40.850, 1.300
SYNCHROTRONESRF ID250.850, 1.300
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.851
21.31
ReflectionResolution: 4.5→257 Å / Num. all: 85991 / % possible obs: 91.1 % / Observed criterion σ(I): -2.5 / Redundancy: 4 % / Rsym value: 12.5
Reflection shellHighest resolution: 4.5 Å / Redundancy: 2 % / % possible all: 91.1
Reflection
*PLUS
Num. obs: 85991 / % possible obs: 93.2 % / Rmerge(I) obs: 0.108
Reflection shell
*PLUS
% possible obs: 91.1 %

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Processing

Software
NameClassification
SHARPphasing
Omodel building
RefinementMethod to determine structure: MIRAS / Resolution: 4.5→30 Å / Num. reflection all: 85991 / Num. reflection obs: 85991 / σ(I): 0
Details: Structure was traced manually and no refinement was carried out. Positioning of ribosomal proteins is tentative. The crystallographically determined structure of an 18 W atom cluster (ref. 3) ...Details: Structure was traced manually and no refinement was carried out. Positioning of ribosomal proteins is tentative. The crystallographically determined structure of an 18 W atom cluster (ref. 3) that belongs to the Wative particle was placed around its center of mass in an arbitrary orientation in order to indicate its volume.
Refinement stepCycle: LAST / Resolution: 4.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms280 3594 82 0 3956
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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