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- PDB-7bfg: Circular permutant of ribosomal protein S6, P54-55 truncated, V37... -

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Basic information

Entry
Database: PDB / ID: 7bfg
TitleCircular permutant of ribosomal protein S6, P54-55 truncated, V37A mutant.
Components30S ribosomal protein S6,30S ribosomal protein S6
KeywordsRIBOSOMAL PROTEIN / Circular permutant / native stacking / / designed amyloid fibril
Function / homology
Function and homology information


rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / 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: 2.01 Å
AuthorsWang, H. / Logan, D.T. / Oliveberg, M.
CitationJournal: To Be Published
Title: Circular permutant of ribosomal protein S6
Authors: Wang, H. / Logan, D.T. / Oliveberg, M.
History
DepositionJan 2, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 13, 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
J: 30S ribosomal protein S6,30S ribosomal protein S6
K: 30S ribosomal protein S6,30S ribosomal protein S6
L: 30S ribosomal protein S6,30S ribosomal protein S6
C: 30S ribosomal protein S6,30S ribosomal protein S6
D: 30S ribosomal protein S6,30S ribosomal protein S6
E: 30S ribosomal protein S6,30S ribosomal protein S6
F: 30S ribosomal protein S6,30S ribosomal protein S6
G: 30S ribosomal protein S6,30S ribosomal protein S6
H: 30S ribosomal protein S6,30S ribosomal protein S6
I: 30S ribosomal protein S6,30S ribosomal protein S6


Theoretical massNumber of molelcules
Total (without water)121,24212
Polymers121,24212
Non-polymers00
Water90150
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15860 Å2
ΔGint5 kcal/mol
Surface area51210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.315, 75.933, 223.737
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 10103.496 Da / Num. of mol.: 12 / Mutation: V37A
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.: 50 / 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: 2.18 Å3/Da / Density % sol: 43.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 0.1 M citrate 20% w/v PEG 6000

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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: P13 (MX1) / Wavelength: 0.97625 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.01→111.87 Å / Num. obs: 45056 / % possible obs: 90.5 % / Redundancy: 6.5 % / CC1/2: 0.996 / Rmerge(I) obs: 0.197 / Rpim(I) all: 0.085 / Rrim(I) all: 0.215 / Net I/σ(I): 6.7
Reflection shell

Num. unique obs: 2253 / Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) all% possible all
2.029-2.2296.81.2470.7010.5131.35172.6
6.576-111.8685.50.0840.9990.0390.09299.7

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Processing

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

1ris


Resolution: 2.01→111.87 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.898 / SU B: 18.151 / SU ML: 0.217 / Cross valid method: FREE R-VALUE / σ(F): 0 / ESU R: 0.585 / ESU R Free: 0.297 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2793 2223 4.9 %RANDOM
Rwork0.2474 ---
obs0.249 42921 62.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 137.63 Å2 / Biso mean: 38.834 Å2 / Biso min: 8.46 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å20 Å20 Å2
2--0.68 Å20 Å2
3----0.29 Å2
Refinement stepCycle: final / Resolution: 2.01→111.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8508 0 0 50 8558
Biso mean---31.4 -
Num. residues----1032
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0138616
X-RAY DIFFRACTIONr_bond_other_d0.0020.0178208
X-RAY DIFFRACTIONr_angle_refined_deg1.3651.65411640
X-RAY DIFFRACTIONr_angle_other_deg1.2741.57718888
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.59951020
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.34420.98612
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.404151608
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.88915120
X-RAY DIFFRACTIONr_chiral_restr0.0760.21056
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.029780
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021908
LS refinement shellResolution: 2.01→2.059 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.512 12 -
Rwork0.331 304 -
obs--6.07 %
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)
12.1268-0.8601-0.51951.60460.28541.767-0.09950.002-0.05560.083-0.01430.029-0.031-0.0240.11380.08440.02640.02510.00970.00380.0655-2.59572.9962195.7529
22.6815-1.3848-0.3572.5715-0.80431.5569-0.01970.0220.05360.031-0.2045-0.1063-0.05540.02890.22420.13950.0396-0.00410.04270.00260.04655.53399.4406214.5543
30.37070.2336-0.90991.15170.72864.07760.02150.17920.02490.19820.0405-0.07910.3572-0.5719-0.0620.1814-0.06090.06150.12030.0120.0872-3.85289.8243140.2351
41.5381.4040.62882.0252-1.47395.9427-0.0942-0.0608-0.0474-0.4166-0.0353-0.10430.8526-0.02170.12950.2244-0.02410.02270.0616-0.02040.0213.9762.7836158.513
52.73840.1035-0.38530.0470.26633.47860.09590.18720.01650.0107-0.0272-0.0408-0.1705-0.1102-0.06870.0953-0.0242-0.00710.05050.04670.0762.389912.535177.4508
60.9219-0.49270.31592.3871-0.64533.09360.0714-0.00840.0049-0.0673-0.09480.13610.0484-0.11380.02340.1143-0.0058-0.00750.0168-0.02340.0495-4.62847.52269.3879
73.194-0.32560.39721.51980.13840.8338-0.07240.02780.0653-0.0219-0.0285-0.0754-0.1007-0.0210.1010.05630.0252-0.01050.06530.02680.03721.310912.797884.2124
82.6543-1.7246-0.11172.716-0.66221.50270.08890.078-0.0611-0.1259-0.18290.10770.1112-0.0430.09390.08270.0368-0.03670.0401-0.03810.0449-6.10755.9376103.0866
91.34790.11410.15242.64880.76731.6020.05-0.03250.02850.0125-0.0322-0.18390.087-0.1186-0.01780.0806-0.006-0.03610.01040.00460.07775.03018.0692120.9897
100.63890.3622-0.0722.7305-0.18611.56160.0063-0.0691-0.042-0.1327-0.0087-0.0594-0.01450.1550.00250.1097-0.05320.00850.0471-0.0050.03525.00514.969628.1192
112.49281.48451.11622.6290.64322.4666-0.2016-0.0057-0.02740.11930.07730.0928-0.1345-0.09190.12430.0709-0.00420.01040.0272-0.00290.0368-2.634313.39745.8519
121.93780.2971-0.90151.4555-0.42562.43610.00470.1347-0.0364-0.1087-0.01220.02810.2303-0.08640.00750.0712-0.00230.00570.1197-0.00070.0035-1.66464.41564.9325
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-39 - 46
2X-RAY DIFFRACTION2B-39 - 46
3X-RAY DIFFRACTION3J-39 - 46
4X-RAY DIFFRACTION4K-39 - 46
5X-RAY DIFFRACTION5L-39 - 46
6X-RAY DIFFRACTION6C-39 - 46
7X-RAY DIFFRACTION7D-39 - 46
8X-RAY DIFFRACTION8E-39 - 46
9X-RAY DIFFRACTION9F-39 - 46
10X-RAY DIFFRACTION10G-39 - 46
11X-RAY DIFFRACTION11H-39 - 46
12X-RAY DIFFRACTION12I-39 - 46

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