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- PDB-1ris: CRYSTAL STRUCTURE OF THE RIBOSOMAL PROTEIN S6 FROM THERMUS THERMO... -

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Basic information

Entry
Database: PDB / ID: 1ris
TitleCRYSTAL STRUCTURE OF THE RIBOSOMAL PROTEIN S6 FROM THERMUS THERMOPHILUS
ComponentsRIBOSOMAL PROTEIN S6
KeywordsRIBOSOMAL PROTEIN
Function / homology
Function and homology information


rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / cytoplasm
Similarity search - Function
Ribosomal protein S6/Translation elongation factor EF1B / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein S6 / Ribosomal protein S6 / Ribosomal protein S6 superfamily / Translation elongation factor EF1B/ribosomal protein S6 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Small ribosomal subunit protein bS6
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsLindahl, M. / Svensson, L.A. / Liljas, A. / Sedelnikova, S.E. / Eliseikina, I.A. / Fomenkova, N.P. / Nevskaya, N. / Nikonov, S.V. / Garber, M.B. / Muranova, T.A. ...Lindahl, M. / Svensson, L.A. / Liljas, A. / Sedelnikova, S.E. / Eliseikina, I.A. / Fomenkova, N.P. / Nevskaya, N. / Nikonov, S.V. / Garber, M.B. / Muranova, T.A. / Rykonova, A.I. / Amons, R.
Citation
#1: Journal: J.Mol.Biol. / Year: 1991
Title: Crystals of Protein S6 from the 30 S Ribosomal Subunit of Thermus Thermophilus
Authors: Sedelnikova, S.E. / Agalarov, S.Ch. / Eliseikina, I.A. / Fomenkova, N.P. / Nikonov, S.V. / Garber, M.B. / Svensson, L.A. / Liljas, A.
History
DepositionMay 31, 1994Processing site: BNL
Revision 1.0Sep 30, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 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

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Assembly

Deposited unit
A: RIBOSOMAL PROTEIN S6


Theoretical massNumber of molelcules
Total (without water)11,9891
Polymers11,9891
Non-polymers00
Water82946
1
A: RIBOSOMAL PROTEIN S6

A: RIBOSOMAL PROTEIN S6

A: RIBOSOMAL PROTEIN S6

A: RIBOSOMAL PROTEIN S6


Theoretical massNumber of molelcules
Total (without water)47,9554
Polymers47,9554
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
crystal symmetry operation3_556-x,y,-z+11
crystal symmetry operation2_565-x,-y+1,z1
Unit cell
Length a, b, c (Å)106.810, 52.720, 41.120
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222

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Components

#1: Protein RIBOSOMAL PROTEIN S6 /


Mass: 11988.753 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / References: UniProt: P23370
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 2.41 Å3/Da / Density % sol: 49.03 %
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
18-15 mg/mlprotein1drop
20.05 MTris-HCl1drop
30.1-0.2 M1dropKF
425 %(v/v)methanepentanediol1reservoir
50.4 M1reservoirNaCl

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2→8 Å / Rfactor Rwork: 0.183 / Rfactor obs: 0.183 / σ(F): 1
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms816 0 0 46 862
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_deg3.2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.85
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
Rfactor obs: 0.183
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 3.2

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