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- PDB-7os7: Circular permutant of ribosomal protein S6, swap helix 2, L75A, A... -

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Basic information

Entry
Database: PDB / ID: 7os7
TitleCircular permutant of ribosomal protein S6, swap helix 2, L75A, A92K mutant
Components30S ribosomal protein S6,30S ribosomal protein S6
KeywordsRIBOSOMAL PROTEIN / Circular permutant / native stacking / / designed amyloid fibril
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: 1.65 Å
AuthorsWang, H. / Logan, D.T. / Oliveberg, M.
CitationJournal: To Be Published
Title: Circular permutant of ribosomal protein S6, swap helix 2, L75A, A92K mutant
Authors: Wang, H. / Logan, D.T. / Oliveberg, M.
History
DepositionJun 8, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 22, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)25,4552
Polymers25,4552
Non-polymers00
Water1,69394
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1740 Å2
ΔGint-2 kcal/mol
Surface area11030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.646, 55.646, 148.561
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

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


Mass: 12727.479 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / Gene: rpsF, TTHA0245 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q5SLP8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 2.24 Å3/Da / Density % sol: 44.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M ammonium citrate dibasic 14% w/v PEG 3350

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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: Oct 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97996 Å / Relative weight: 1
ReflectionResolution: 1.65→148.56 Å / Num. obs: 29194 / % possible obs: 99.7 % / Redundancy: 8.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.024 / Rrim(I) all: 0.072 / Net I/σ(I): 15.9 / Num. measured all: 253548 / Scaling rejects: 5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.65-1.6791.2881288014380.8020.451.367298.8
8.86-148.5660.05214302390.9930.0220.05733.995.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
Aimless0.6.2data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ris

1ris


Resolution: 1.65→52.11 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.953 / SU B: 4.33 / SU ML: 0.065 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.108 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2286 1468 5 %RANDOM
Rwork0.1614 ---
obs0.1647 27668 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 146.42 Å2 / Biso mean: 37.531 Å2 / Biso min: 17.42 Å2
Baniso -1Baniso -2Baniso -3
1-1.23 Å20 Å20 Å2
2--1.23 Å20 Å2
3----2.46 Å2
Refinement stepCycle: final / Resolution: 1.65→52.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1706 0 0 94 1800
Biso mean---40.67 -
Num. residues----206
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0131737
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171687
X-RAY DIFFRACTIONr_angle_refined_deg1.6961.6592350
X-RAY DIFFRACTIONr_angle_other_deg1.3861.5813883
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2455206
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.98720.407123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.88915327
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4451526
X-RAY DIFFRACTIONr_chiral_restr0.0810.2215
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021959
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02387
X-RAY DIFFRACTIONr_rigid_bond_restr6.66533424
LS refinement shellResolution: 1.65→1.688 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.285 103 -
Rwork0.242 1990 -
obs--98.4 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.5889-0.0712-0.07360.02350.08480.7325-0.0508-0.0120.0170.00730.01020.02630.04520.09350.04060.09610.00790.0110.0125-0.00140.090922.0331-3.6445-16.4925
20.3088-0.28650.54931.00780.49942.45890.01950.0979-0.0317-0.00240.02030.05840.09840.43-0.03980.05820.01910.00010.1497-0.02170.027232.1525-0.45431.5789
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 108
2X-RAY DIFFRACTION2B8 - 108

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