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- PDB-1an7: RIBOSOMAL PROTEIN S8 FROM THERMUS THERMOPHILUS -

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Basic information

Entry
Database: PDB / ID: 1an7
TitleRIBOSOMAL PROTEIN S8 FROM THERMUS THERMOPHILUS
ComponentsRIBOSOMAL PROTEIN S8
KeywordsRIBOSOMAL PROTEIN / RRNA-PROTEIN BINDING / PROTEIN-PROTEIN BINDING / THERMUS THERMOPHILUS
Function / homology
Function and homology information


rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / cytoplasm
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 / Ribosomal protein S8 superfamily / Ribosomal protein S8 / Ribosomal protein S8 signature. / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Small ribosomal subunit protein uS8
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.9 Å
AuthorsNevskaya, N. / Nikonov, S. / Al-Karadaghi, S.
Citation
Journal: J.Mol.Biol. / Year: 1998
Title: Crystal structure of ribosomal protein S8 from Thermus thermophilus reveals a high degree of structural conservation of a specific RNA binding site.
Authors: Nevskaya, N. / Tishchenko, S. / Nikulin, A. / al-Karadaghi, S. / Liljas, A. / Ehresmann, B. / Ehresmann, C. / Garber, M. / Nikonov, S.
#1: Journal: Proteins / Year: 1997
Title: Crystallization and Preliminary Crystallographic Analysis of Ribosomal Protein S8 from Thermus Thermophilus
Authors: Tishchenko, S.V. / Vysotskaya, V.S. / Fomenkova, N.P. / Nikonov, S.V. / Ehresmann, B. / Garber, M.B.
History
DepositionJun 27, 1997Processing site: BNL
Revision 1.0Jul 1, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)31,2482
Polymers31,2482
Non-polymers00
Water0
1
A: RIBOSOMAL PROTEIN S8
B: RIBOSOMAL PROTEIN S8

A: RIBOSOMAL PROTEIN S8
B: RIBOSOMAL PROTEIN S8


Theoretical massNumber of molelcules
Total (without water)62,4974
Polymers62,4974
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Unit cell
Length a, b, c (Å)67.860, 67.860, 174.090
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.8928, 0.0842, -0.4425), (0.1368, -0.8852, -0.4446), (-0.4292, -0.4575, 0.7788)
Vector: 84.1617, 74.8639, 39.3939)

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Components

#1: Protein RIBOSOMAL PROTEIN S8 /


Mass: 15624.214 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: VK1 / Cell line: BL21 / Gene: RPS8 / Plasmid: PET-TTHS8 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P24319

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.21 Å3/Da / Density % sol: 60 %
Crystal growpH: 6 / Details: pH 6.0
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 24 ℃ / Method: vapor diffusion, hanging drop
Details: Tishchenko, S.V., (1997) Proteins: Struct.,Funct., Genet., 27, 309.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
125-30 mg/mlprotein1drop
240 mMpotassium phosphate1drop
31 mMdithiothreitol1drop
440 %satammonium sulfate1reservoir
57 %(v/v)MPD1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Feb 10, 1996
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.9→20 Å / Num. obs: 8932 / % possible obs: 94.5 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 33.6 Å2 / Rmerge(I) obs: 0.051
Reflection shellResolution: 2.9→2.95 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.019 / % possible all: 93.6

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MIR / Resolution: 2.9→8 Å
RfactorNum. reflection% reflectionSelection details
Rfree0.275 871 10 %RANDOM
Rwork0.162 ---
obs0.162 8932 --
Displacement parametersBiso mean: 37 Å2
Refinement stepCycle: LAST / Resolution: 2.9→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2200 0 0 0 2200
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
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_deg3.477
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.29
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.432
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
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.291
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.432

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