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- PDB-6i6u: Circular permutant of ribosomal protein S6, adding 9aa to N termi... -

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Basic information

Entry
Database: PDB / ID: 6i6u
TitleCircular permutant of ribosomal protein S6, adding 9aa to N terminal of P81-82, L75A mutant
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 / 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 HB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 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
B: 30S ribosomal protein S6,30S ribosomal protein S6


Theoretical massNumber of molelcules
Total (without water)24,6002
Polymers24,6002
Non-polymers00
Water1,802100
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3120 Å2
ΔGint-16 kcal/mol
Surface area11280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.910, 43.920, 70.630
Angle α, β, γ (deg.)90.000, 117.180, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein 30S ribosomal protein S6,30S ribosomal protein S6 / TS9 / TS9


Mass: 12300.046 Da / Num. of mol.: 2
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.: 100 / 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: 2.04 Å3/Da / Density % sol: 39.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Calcium chloride dehydrate 0.1 M Tris pH 8.0 20% w/v PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.97999 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 31, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97999 Å / Relative weight: 1
ReflectionResolution: 1.57→62.83 Å / Num. obs: 28101 / % possible obs: 99.9 % / Redundancy: 6.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.03 / Rrim(I) all: 0.077 / Net I/σ(I): 11.9 / Num. measured all: 188024 / Scaling rejects: 7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.57-1.596.80.94313670.7720.391.022100
8.58-62.834.70.0511580.9960.0250.05786.3

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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: 1.57→62.83 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.277 / SU ML: 0.081 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.1 / ESU R Free: 0.106
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2563 1409 5 %RANDOM
Rwork0.2079 ---
obs0.2103 26699 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 101.11 Å2 / Biso mean: 33.166 Å2 / Biso min: 15.91 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å20 Å2-0.7 Å2
2--2.35 Å20 Å2
3----0.99 Å2
Refinement stepCycle: final / Resolution: 1.57→62.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1683 0 0 100 1783
Biso mean---37.02 -
Num. residues----204
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0191707
X-RAY DIFFRACTIONr_bond_other_d0.0020.021648
X-RAY DIFFRACTIONr_angle_refined_deg2.1211.9862310
X-RAY DIFFRACTIONr_angle_other_deg1.13433791
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2855202
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.04823.26395
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.55315316
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.941525
X-RAY DIFFRACTIONr_chiral_restr0.1230.2256
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211895
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02354
LS refinement shellResolution: 1.566→1.607 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 101 -
Rwork0.303 1947 -
all-2048 -
obs--99.95 %

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