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- PDB-1pkp: THE STRUCTURE OF RIBOSOMAL PROTEIN S5 REVEALS SITES OF INTERACTIO... -

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Basic information

Entry
Database: PDB / ID: 1pkp
TitleTHE STRUCTURE OF RIBOSOMAL PROTEIN S5 REVEALS SITES OF INTERACTION WITH 16S RRNA
ComponentsRIBOSOMAL PROTEIN S5
KeywordsRIBOSOMAL PROTEIN
Function / homology
Function and homology information


small ribosomal subunit / rRNA binding / structural constituent of ribosome / translation / response to antibiotic
Similarity search - Function
Double Stranded RNA Binding Domain - #20 / Ribosomal Protein S5; domain 2 - #10 / Ribosomal Protein S5; domain 2 / Double Stranded RNA Binding Domain / Ribosomal protein S5, bacterial-type / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S5 signature. / Ribosomal protein S5 / S5 double stranded RNA-binding domain profile. / Ribosomal protein S5, N-terminal ...Double Stranded RNA Binding Domain - #20 / Ribosomal Protein S5; domain 2 - #10 / Ribosomal Protein S5; domain 2 / Double Stranded RNA Binding Domain / Ribosomal protein S5, bacterial-type / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S5 signature. / Ribosomal protein S5 / S5 double stranded RNA-binding domain profile. / Ribosomal protein S5, N-terminal / Ribosomal protein S5, C-terminal / Ribosomal protein S5, N-terminal domain / Ribosomal protein S5, C-terminal domain / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Small ribosomal subunit protein uS5
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.8 Å
AuthorsRamakrishnan, V. / White, S.W.
Citation
Journal: Nature / Year: 1992
Title: The structure of ribosomal protein S5 reveals sites of interaction with 16S rRNA.
Authors: Ramakrishnan, V. / White, S.W.
#1: Journal: J.Mol.Biol. / Year: 1988
Title: Model for the Three-Dimensional Folding of 16S Ribosomal RNA
Authors: Stern, S. / Weiser, B. / Noller, H.F.
#2: Journal: FEBS Lett. / Year: 1983
Title: Proteins of the Bacillus Stearothermophilus Ribosome: A 5A Structure Analysis of Protein S5
Authors: White, S.W. / Appelt, K. / Dijk, J. / Wilson, K.S.
#3: Journal: J.Biol.Chem. / Year: 1983
Title: Proteins of the Bacillus Stearothermophilus Ribosome. Crystallization of Proteins L30 and S5
Authors: Appelt, K. / White, S.W. / Wilson, K.S.
#4: Journal: Mol.Gen.Genet. / Year: 1975
Title: Effect of Different Mutations in Ribosomal Protein S5 of Escherichia Coli on Translational Fidelity
Authors: Piepersberg, W. / Bock, A. / Wittmann, H.-G.
#5: Journal: Mol.Gen.Genet. / Year: 1975
Title: Genetic Position and Amino Acid Replacements of Several Mutations in Ribosomal Protein S5 from Escherichia Coli
Authors: Piepersberg, W. / Bock, A. / Yaguchi, M. / Wittmann, H.-G.
History
DepositionAug 30, 1993Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RIBOSOMAL PROTEIN S5


Theoretical massNumber of molelcules
Total (without water)15,9151
Polymers15,9151
Non-polymers00
Water00
1
A: RIBOSOMAL PROTEIN S5

A: RIBOSOMAL PROTEIN S5


Theoretical massNumber of molelcules
Total (without water)31,8292
Polymers31,8292
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Unit cell
Length a, b, c (Å)59.300, 59.300, 109.800
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein RIBOSOMAL PROTEIN S5


Mass: 15914.577 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: BACILLUS STEAROTHERMOPHILUS / Gene (production host): BACILLUS STEAROTHERMOPHILUS / References: UniProt: P02357

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.5 Å3/Da / Density % sol: 64.86 %
Crystal grow
*PLUS
Method: unknown / PH range low: 8.2 / PH range high: 7.2
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
15-10 mg/mlprotein11
21.2 Mphosphate12(NaH2PO4/K2HPO4 mixture)

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.7 Å / Num. obs: 5829 / Num. measured all: 14806 / Rmerge(I) obs: 0.051

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.8→6 Å / Rfactor Rwork: 0.22 / Rfactor obs: 0.22 / σ(F): 0
Refinement stepCycle: LAST / Resolution: 2.8→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1071 0 0 0 1071
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.74
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 6 Å / σ(F): 0 / Rfactor all: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 3.74

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