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- PDB-6i6y: Circular permutant of ribosomal protein S6, swap helix 2 -

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Basic information

Entry
Database: PDB / ID: 6i6y
TitleCircular permutant of ribosomal protein S6, swap helix 2
Components30S ribosomal protein S6,30S ribosomal protein S6
KeywordsRIBOSOMAL PROTEIN / Circular permutant / strand swap / local 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 HB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 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 1.1Dec 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 1.2Jan 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 S6,30S ribosomal protein S6


Theoretical massNumber of molelcules
Total (without water)12,8431
Polymers12,8431
Non-polymers00
Water905
1
A: 30S ribosomal protein S6,30S ribosomal protein S6

A: 30S ribosomal protein S6,30S ribosomal protein S6


Theoretical massNumber of molelcules
Total (without water)25,6852
Polymers25,6852
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area1980 Å2
ΔGint-10 kcal/mol
Surface area10960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.810, 34.810, 134.190
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 S6,30S ribosomal protein S6 / TS9 / TS9


Mass: 12842.653 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB8 (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.: 5 / 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: 32.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.02 M Magnesium chloride hexahydrate 0.1 M HEPES 7.5 pH 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: MAX IV / Beamline: BioMAX / Wavelength: 0.97996 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97996 Å / Relative weight: 1
ReflectionResolution: 2.15→134.19 Å / Num. obs: 5024 / % possible obs: 100 % / Redundancy: 11.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.039 / Rrim(I) all: 0.129 / Net I/σ(I): 9.3 / Num. measured all: 57725 / Scaling rejects: 3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.15-2.2212.71.3644220.7890.3921.421100
8.88-134.196.90.0771040.9990.0270.08298.3

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Processing

Software
NameVersionClassification
Aimless0.6.2data scaling
REFMAC5.8.0189refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Ris

1ris


Resolution: 2.15→33.69 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.929 / SU B: 8.249 / SU ML: 0.209 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.353 / ESU R Free: 0.24 / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2681 244 4.9 %RANDOM
Rwork0.2283 ---
obs0.2303 4726 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 178.48 Å2 / Biso mean: 65.968 Å2 / Biso min: 42.26 Å2
Baniso -1Baniso -2Baniso -3
1-1.33 Å20 Å20 Å2
2--1.33 Å20 Å2
3----2.66 Å2
Refinement stepCycle: final / Resolution: 2.15→33.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms782 0 0 5 787
Biso mean---72.64 -
Num. residues----95
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.019794
X-RAY DIFFRACTIONr_angle_refined_deg1.7711.9771074
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.873594
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.50523.40944
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.39215145
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.3481511
X-RAY DIFFRACTIONr_chiral_restr0.1050.2119
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021608
LS refinement shellResolution: 2.153→2.209 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 20 -
Rwork0.311 331 -
all-351 -
obs--100 %

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