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- PDB-1sei: STRUCTURE OF 30S RIBOSOMAL PROTEIN S8 -

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Basic information

Entry
Database: PDB / ID: 1sei
TitleSTRUCTURE OF 30S RIBOSOMAL PROTEIN S8
ComponentsRIBOSOMAL PROTEIN S8
KeywordsRIBOSOMAL PROTEIN / PROKARYOTIC / RRNA-BINDING
Function / homology
Function and homology information


rRNA binding / ribosome / structural constituent of ribosome / translation
Similarity search - Function
Ribosomal Protein S8; Chain: A, domain 1 - #30 / Dna Ligase; domain 1 - #10 / Ribosomal Protein S8; Chain: A, domain 1 / Dna Ligase; domain 1 / Ribosomal protein S8 signature. / Ribosomal protein S8 / Ribosomal protein S8 superfamily / Ribosomal protein S8 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
30S ribosomal protein S8
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsDavies, C. / Ramakrishnan, V. / White, S.W.
CitationJournal: Structure / Year: 1996
Title: Structural evidence for specific S8-RNA and S8-protein interactions within the 30S ribosomal subunit: ribosomal protein S8 from Bacillus stearothermophilus at 1.9 A resolution.
Authors: Davies, C. / Ramakrishnan, V. / White, S.W.
History
DepositionAug 14, 1996Processing site: BNL
Revision 1.0Mar 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RIBOSOMAL PROTEIN S8
B: RIBOSOMAL PROTEIN S8


Theoretical massNumber of molelcules
Total (without water)29,3062
Polymers29,3062
Non-polymers00
Water2,108117
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.160, 85.960, 39.590
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.9987, 0.04913, 0.01345), (0.04932, 0.99869, 0.01369), (-0.01276, 0.01433, -0.99982)
Vector: 77.66786, -2.45282, 19.76353)

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Components

#1: Protein RIBOSOMAL PROTEIN S8


Mass: 14653.166 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Description: T7 EXPRESSION SYSTEM INDUCIBLE BY ISOPROPYL-BETA-D-THIOGALACTOPYRANOSIDE (IPTG). ALSO SEE MEDLINE IDENTIFIER 92110431.
Gene: BACILLUS STEAROTHERMOPHILUS / Plasmid: PET13 / Species (production host): Escherichia coli / Gene (production host): BACILLUS STEAROTHERMOPHILUS / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P56209
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47.3 %
Crystal grow
*PLUS
Temperature: 22 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
Common name: sodium chloride

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jun 7, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 21973 / % possible obs: 94.2 % / Observed criterion σ(I): 0 / Redundancy: 5.05 % / Rmerge(I) obs: 0.083
Reflection
*PLUS
Highest resolution: 1.9 Å

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
X-PLORphasing
RefinementResolution: 1.9→8 Å / σ(F): 0
RfactorNum. reflection
Rfree0.288 -
Rwork0.222 -
obs0.222 21545
Displacement parametersBiso mean: 27.7 Å2
Refinement stepCycle: LAST / Resolution: 1.9→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2058 0 0 117 2175
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
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_deg1.77
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.474
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it1.5
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.474
LS refinement shell
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 2 Å / % reflection Rfree: 0.35 % / Total num. of bins used: 8 / Rfactor obs: 0.31

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