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- PDB-6i6e: Circular permutant of ribosomal protein S6, swap strand 1 , L10A ... -

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Basic information

Entry
Database: PDB / ID: 6i6e
TitleCircular permutant of ribosomal protein S6, swap strand 1 , L10A mutant
Components30S ribosomal protein S6
KeywordsRIBOSOMAL PROTEIN / Circular permutant / strand swap / globling unfolding / cis-proline. / designed protein
Function / homology
Function and homology information


small ribosomal subunit rRNA binding / structural constituent of ribosome / 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 / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / atom_type / entity / entity_src_gen / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_unobs_or_zero_occ_residues / 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 / software / struct_mon_prot_cis
Item: _entity.pdbx_number_of_molecules / _entity_src_gen.gene_src_strain ..._entity.pdbx_number_of_molecules / _entity_src_gen.gene_src_strain / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_assembly.details / _pdbx_struct_assembly_prop.value / _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_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_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.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_B_iso_mean_solvent / _refine_hist.pdbx_number_atoms_protein / _refine_hist.pdbx_number_residues_total / _software.classification / _software.name / _software.version / _struct_mon_prot_cis.pdbx_omega_angle
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

Downloads & links

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Assembly

Deposited unit
A: 30S ribosomal protein S6


Theoretical massNumber of molelcules
Total (without water)12,4881
Polymers12,4881
Non-polymers00
Water1,38777
1
A: 30S ribosomal protein S6

A: 30S ribosomal protein S6


Theoretical massNumber of molelcules
Total (without water)24,9762
Polymers24,9762
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_465y-1,x+1,-z1
Buried area2140 Å2
ΔGint-8 kcal/mol
Surface area10480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.870, 34.870, 135.149
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein 30S ribosomal protein S6 / TS9


Mass: 12488.207 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.: 77 / 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: 32.83 %
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: 0.9763 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: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.2→45.05 Å / Num. obs: 27269 / % possible obs: 100 % / Redundancy: 24.2 % / CC1/2: 1 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.012 / Rrim(I) all: 0.061 / Net I/σ(I): 23.5 / Num. measured all: 658750 / Scaling rejects: 122
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.2-1.22240.65412960.8410.1350.668100
6.57-45.0515.90.0472280.9980.0130.04996.2

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
Aimless0.5.27data scaling
PDB_EXTRACT3.24data extraction
iMOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Ris

1ris


Resolution: 1.2→33.79 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.5 / Phase error: 13.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1627 1337 4.92 %RANDOM
Rwork0.1447 25839 --
obs0.1455 27176 99.96 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 101.52 Å2 / Biso mean: 23.5671 Å2 / Biso min: 11.36 Å2
Refinement stepCycle: final / Resolution: 1.2→33.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms783 0 0 77 860
Biso mean---31.92 -
Num. residues----95
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.2-1.240.23111400.220124882628
1.24-1.290.21221300.184725282658
1.29-1.350.17161260.159825252651
1.35-1.420.17791170.149825552672
1.42-1.510.15181490.114725372686
1.51-1.630.1531420.109325372679
1.63-1.790.14291410.11525652706
1.79-2.050.1351420.115326362778
2.05-2.580.15461280.128426182746
2.59-33.790.17641220.167828502972

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