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- PDB-6i69: Circular permutant of ribosomal protein S6, adding 5aa to C termi... -

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Basic information

Entry
Database: PDB / ID: 6i69
TitleCircular permutant of ribosomal protein S6, adding 5aa to C terminal of P97-3, L10A mutant
Components30S ribosomal protein S6
KeywordsRIBOSOMAL PROTEIN / Circular permutant / strand swap / globling unfolding / cis-proline.
Function / homology
Function and homology information


rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / cytoplasm
Similarity search - Function
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
Similarity search - Domain/homology
Small ribosomal subunit protein bS6
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsWang, H. / Logan, D.T. / Oliveberg, M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Exposing the distinctive modular behavior of beta-strands and alpha-helices in folded proteins.
Authors: Wang, H. / Logan, D.T. / Danielsson, J. / Oliveberg, M.
History
DepositionNov 15, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 27, 2019Provider: repository / Type: Initial release
Revision 2.0Jul 22, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / atom_sites / atom_type / cell / entity / entity_src_gen / pdbx_nonpoly_scheme / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_sheet_hbond / pdbx_struct_special_symmetry / pdbx_validate_close_contact / pdbx_validate_planes / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_symm_contact / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns / software / struct_mon_prot_cis / symmetry
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _cell.volume / _entity.pdbx_number_of_molecules / _entity_src_gen.gene_src_strain / _pdbx_struct_assembly.details / _pdbx_struct_assembly_prop.value / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.aniso_B[1][1] / _refine.aniso_B[1][2] / _refine.aniso_B[1][3] / _refine.aniso_B[2][2] / _refine.aniso_B[2][3] / _refine.aniso_B[3][3] / _refine.correlation_coeff_Fo_to_Fc / _refine.correlation_coeff_Fo_to_Fc_free / _refine.details / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_d_res_low / _refine.ls_number_reflns_R_work / _refine.ls_number_reflns_obs / _refine.ls_percent_reflns_R_free / _refine.overall_SU_B / _refine.overall_SU_ML / _refine.pdbx_ls_cross_valid_method / _refine.pdbx_ls_sigma_F / _refine.pdbx_overall_ESU_R / _refine.pdbx_overall_ESU_R_Free / _refine.pdbx_overall_phase_error / _refine.pdbx_solvent_ion_probe_radii / _refine.pdbx_solvent_shrinkage_radii / _refine.pdbx_solvent_vdw_probe_radii / _refine.pdbx_stereochemistry_target_values / _refine.solvent_model_details / _refine_hist.cycle_id / _refine_hist.d_res_low / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_B_iso_mean_solvent / _refine_hist.pdbx_number_residues_total / _reflns.B_iso_Wilson_estimate / _struct_mon_prot_cis.pdbx_omega_angle / _symmetry.space_group_name_Hall
Description: Polymer geometry / Details: non-planar carboxylate groups in the side chains / Provider: author / Type: Coordinate replacement
Revision 2.1Dec 9, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: 30S ribosomal protein S6


Theoretical massNumber of molelcules
Total (without water)11,8801
Polymers11,8801
Non-polymers00
Water1,60389
1
A: 30S ribosomal protein S6

A: 30S ribosomal protein S6


Theoretical massNumber of molelcules
Total (without water)23,7592
Polymers23,7592
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_465y-1,x+1,-z1
Buried area2240 Å2
ΔGint-9 kcal/mol
Surface area10500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.810, 34.810, 135.177
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Components on special symmetry positions
IDModelComponents
11A-217-

HOH

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Components

#1: Protein 30S ribosomal protein S6 / TS9


Mass: 11879.521 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Gene: rpsF, TTHA0245 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q5SLP8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / Source method: isolated from a natural source / Formula: H2O

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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

CrystalDensity Matthews: 1.83 Å3/Da / Density % sol: 32.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.02 M Magnesium chloride hexahydrate 0.1 M HEPES pH 7.5 22% w/v Poly (acrylic acid sodium salt) 5100

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.97626 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 1.2→34.81 Å / Num. obs: 27159 / % possible obs: 99.7 % / Redundancy: 24.2 % / Biso Wilson estimate: 15.38 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.012 / Rrim(I) all: 0.058 / Net I/σ(I): 26.7 / Num. measured all: 657721 / Scaling rejects: 56
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.2-1.2223.80.48212790.9430.0990.49399.2
6.56-34.8117.50.0461930.9990.0110.04788.8

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PHENIX1.17.1_3660refinement
Aimless0.5.32data scaling
PDB_EXTRACT3.24data extraction
iMOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Ris

1ris


Resolution: 1.2→33.71 Å / SU ML: 0.1147 / Cross valid method: FREE R-VALUE / σ(F): 1.51 / Phase error: 14.6007
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.1686 1337 4.94 %RANDOM
Rwork0.1371 25753 --
obs0.1386 27090 99.47 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.35 Å2
Refinement stepCycle: LAST / Resolution: 1.2→33.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms787 0 0 89 876
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0118861
X-RAY DIFFRACTIONf_angle_d1.14921181
X-RAY DIFFRACTIONf_chiral_restr0.0883133
X-RAY DIFFRACTIONf_plane_restr0.0077158
X-RAY DIFFRACTIONf_dihedral_angle_d28.2539360
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.240.20391440.15872480X-RAY DIFFRACTION99.62
1.24-1.290.17881280.14032541X-RAY DIFFRACTION100
1.29-1.350.19311270.13262518X-RAY DIFFRACTION100
1.35-1.420.18361160.13182563X-RAY DIFFRACTION100
1.42-1.510.16681500.11182534X-RAY DIFFRACTION99.93
1.51-1.630.15441430.10142544X-RAY DIFFRACTION99.96
1.63-1.790.16521400.1122568X-RAY DIFFRACTION99.85
1.79-2.050.14521390.10832624X-RAY DIFFRACTION99.57
2.05-2.580.16441290.12952600X-RAY DIFFRACTION98.95
2.58-33.710.1781210.16422781X-RAY DIFFRACTION97.12

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