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- PDB-7bfc: Circular permutant of ribosomal protein S6, P54-55 truncated, -

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Basic information

Entry
Database: PDB / ID: 7bfc
TitleCircular permutant of ribosomal protein S6, P54-55 truncated,
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: 2.13 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
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: 30S ribosomal protein S6,30S ribosomal protein S6
N: 30S ribosomal protein S6,30S ribosomal protein S6
B: 30S ribosomal protein S6,30S ribosomal protein S6
M: 30S ribosomal protein S6,30S ribosomal protein S6
A: 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
I: 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
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
F: 30S ribosomal protein S6,30S ribosomal protein S6


Theoretical massNumber of molelcules
Total (without water)141,84214
Polymers141,84214
Non-polymers00
Water4,792266
1
C: 30S ribosomal protein S6,30S ribosomal protein S6
B: 30S ribosomal protein S6,30S ribosomal protein S6
A: 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
G: 30S ribosomal protein S6,30S ribosomal protein S6
F: 30S ribosomal protein S6,30S ribosomal protein S6


Theoretical massNumber of molelcules
Total (without water)70,9217
Polymers70,9217
Non-polymers00
Water1267
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
N: 30S ribosomal protein S6,30S ribosomal protein S6
M: 30S ribosomal protein S6,30S ribosomal protein S6
I: 30S ribosomal protein S6,30S ribosomal protein S6
H: 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


Theoretical massNumber of molelcules
Total (without water)70,9217
Polymers70,9217
Non-polymers00
Water1267
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.381, 73.582, 115.796
Angle α, β, γ (deg.)90.000, 99.980, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 10131.550 Da / Num. of mol.: 14
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.: 266 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.53 Å3/Da / Density % sol: 51.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES pH 7.5 10% w/v PEG 8000 8% v/v ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.98013 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: 0.98013 Å / Relative weight: 1
ReflectionResolution: 2.13→47.9 Å / Num. obs: 78707 / % possible obs: 99.4 % / Redundancy: 3.4 % / CC1/2: 0.995 / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.08 / Rrim(I) all: 0.15 / Net I/σ(I): 8.3
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
2.13-2.23.51.3242659476950.4110.831.5671.299.6
8.25-47.7230.067425314110.9930.0430.0831.198.3

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Processing

Software
NameVersionClassification
Aimless0.5.21data scaling
REFMAC5.8.0238refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Ris

1ris


Resolution: 2.13→47.77 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.932 / SU B: 18.779 / SU ML: 0.216 / Cross valid method: FREE R-VALUE / σ(F): 0 / ESU R: 0.269 / ESU R Free: 0.214 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2665 3862 4.9 %RANDOM
Rwork0.2268 ---
obs0.2287 74709 99.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 159.02 Å2 / Biso mean: 47.987 Å2 / Biso min: 21.99 Å2
Baniso -1Baniso -2Baniso -3
1--0.46 Å20 Å2-1.19 Å2
2--0.47 Å20 Å2
3---0.39 Å2
Refinement stepCycle: final / Resolution: 2.13→47.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9908 0 0 266 10174
Biso mean---45.81 -
Num. residues----1200
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01310034
X-RAY DIFFRACTIONr_bond_other_d0.0010.0179596
X-RAY DIFFRACTIONr_angle_refined_deg1.9011.65113554
X-RAY DIFFRACTIONr_angle_other_deg1.5311.57722078
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.54551186
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.49120.98714
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.561151878
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.51315140
X-RAY DIFFRACTIONr_chiral_restr0.1090.21228
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211270
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022222
LS refinement shellResolution: 2.13→2.185 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 297 -
Rwork0.344 5422 -
all-5719 -
obs--98.01 %
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)
11.0002-0.2751-0.33570.97610.23360.98610.0058-0.00240.05670.0430.03130.0290.06370.0741-0.03710.03320.01190.03710.1685-0.01060.05723.7-4.10540.761
21.1106-0.07070.25182.473-0.17750.4970.01280.02310.0040.0591-0.0309-0.05240.01870.02160.01810.0095-0.00280.02270.1484-0.01040.079720.23225.46-40.823
31.059-0.4556-0.64681.41440.15090.87650.02720.00630.0696-0.0527-0.044-0.06260.01080.04990.01680.02330.00990.02280.1512-0.00230.065741.250.93951.652
41.12560.8795-0.11492.77880.63011.23290.0846-0.05310.09090.1373-0.17010.11640.1080.01550.08550.0405-0.04380.0230.1790.0090.023221.38830.533-20.103
50.954-0.4642-0.25832.86360.32250.4242-0.011-0.0696-0.00340.126-0.06230.00480.0626-0.02690.07340.0383-0.01330.01620.14380.01560.051442.4010.51373.037
61.4029-0.32770.23581.0201-0.12390.91740.03780.01620.0597-0.0909-0.08970.007-0.08150.09180.0520.0478-0.00870.03210.19190.00210.051819.5044.39521.506
71.45860.4524-0.19250.7105-0.10582.4843-0.13980.097-0.0629-0.09270.0640.09470.27090.05010.07580.0437-0.00430.00490.2033-0.01210.03089.015-5.585.712
81.225-0.2668-0.04341.52360.9991.7386-0.0122-0.01490.0732-0.0990.105-0.0812-0.04310.1562-0.09280.0155-0.00910.02650.1755-0.01250.083165.46130.17641.435
93.37660.89682.45411.2265-0.33762.9452-0.60330.05090.7665-0.07370.02230.2931-0.3766-0.03690.58090.2465-0.0891-0.03890.13620.0080.2731-2.5584.092-9.146
101.8505-1.14530.00171.99360.31740.52760.0546-0.0117-0.11290.02860.03150.14630.00420.0779-0.08610.01230.00320.02360.1483-0.00850.093567.12425.68162.265
111.51-0.2746-0.43161.23840.60281.45810.04550.07050.05090.0304-0.0640.02110.1335-0.03820.01850.03820.00040.03020.1930.01060.034850.721.76428.515
123.45311.0145-0.5511.2219-0.11042.54470.04660.35790.29610.00230.1824-0.0754-0.3962-0.5826-0.22890.06250.080.03120.35340.10730.080442.35232.61111.957
134.90491.95250.07421.32730.36490.72510.144-0.3792-0.398-0.0564-0.0548-0.18320.2190.0874-0.08910.1847-0.0087-0.04390.30340.10140.067535.46322.601-6.004
141.91170.28171.93262.8706-1.67473.3224-0.0160.25580.31240.1823-0.4558-0.1519-0.14040.58450.47190.0276-0.0506-0.02450.27230.10810.1296-5.908-4.077-28.806
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1C-39 - 46
2X-RAY DIFFRACTION2N-39 - 46
3X-RAY DIFFRACTION3B-39 - 46
4X-RAY DIFFRACTION4M-38 - 46
5X-RAY DIFFRACTION5A-39 - 46
6X-RAY DIFFRACTION6D-39 - 46
7X-RAY DIFFRACTION7E-39 - 46
8X-RAY DIFFRACTION8I-39 - 46
9X-RAY DIFFRACTION9G-39 - 46
10X-RAY DIFFRACTION10H-39 - 46
11X-RAY DIFFRACTION11J-38 - 46
12X-RAY DIFFRACTION12K-38 - 46
13X-RAY DIFFRACTION13L-39 - 46
14X-RAY DIFFRACTION14F-38 - 46

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