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- PDB-7bfe: Circular permutant of ribosomal protein S6, P54-55 truncated, L21... -

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Basic information

Entry
Database: PDB / ID: 7bfe
TitleCircular permutant of ribosomal protein S6, P54-55 truncated, L21A 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
IODIDE ION / Small ribosomal subunit protein bS6
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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 / Item: _pdbx_entry_details.has_protein_modification

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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
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,29812
Polymers60,5376
Non-polymers7616
Water1,20767
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7410 Å2
ΔGint-7 kcal/mol
Surface area26120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.000, 67.490, 221.950
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: 10089.470 Da / Num. of mol.: 6 / Mutation: L21A
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: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: I
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.41 Å3/Da / Density % sol: 49.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M sodium iodide 0.1 M Bis-Tris propane 20% w/v PEG 3350

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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: Sep 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.95→64.9 Å / Num. obs: 42847 / % possible obs: 98 % / Redundancy: 2.9 % / CC1/2: 0.989 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.043 / Rrim(I) all: 0.079 / Net I/σ(I): 8
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
1.95-230.404875629530.8870.2710.4892.298.8
8.94-64.572.60.03613175080.9860.0270.04519.392.7

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Processing

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

1ris


Resolution: 1.95→64.65 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.92 / SU B: 13.442 / SU ML: 0.174 / Cross valid method: FREE R-VALUE / σ(F): 0 / ESU R: 0.197 / ESU R Free: 0.181 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2804 2156 5 %RANDOM
Rwork0.2327 ---
obs0.235 40628 97.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 109.04 Å2 / Biso mean: 41.247 Å2 / Biso min: 18.82 Å2
Baniso -1Baniso -2Baniso -3
1-2.5 Å20 Å20 Å2
2--1.02 Å20 Å2
3----3.53 Å2
Refinement stepCycle: final / Resolution: 1.95→64.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4162 0 6 67 4235
Biso mean--53.87 39.37 -
Num. residues----507
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0134216
X-RAY DIFFRACTIONr_bond_other_d0.0020.0174005
X-RAY DIFFRACTIONr_angle_refined_deg1.9451.6525702
X-RAY DIFFRACTIONr_angle_other_deg1.3741.5779216
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6575501
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.73721.141298
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.17415773
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7531557
X-RAY DIFFRACTIONr_chiral_restr0.0940.2519
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024777
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02930
LS refinement shellResolution: 1.95→2.001 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 169 -
Rwork0.356 2912 -
all-3081 -
obs--98.59 %
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)
10.8202-0.08720.75610.48870.07820.79450.0129-0.03-0.0488-0.05910.04130.0116-0.05260.0485-0.05410.14440.00870.00690.19750.01260.0279-15.1389-10.226210.0474
20.6025-0.35910.30661.0108-0.13261.11770.01510.05490.0275-0.0203-0.128-0.144-0.09860.07990.11290.1501-0.0005-0.00280.16990.01250.053-9.425-3.586929.5807
30.8487-0.1052-0.29331.3076-0.24460.18110.00260.04270.0303-0.05640.02650.06470.04670.0145-0.02910.1762-0.0378-0.00730.1872-0.03360.0183-14.78975.209684.0174
41.49430.72520.32494.8259-0.0790.20220.0018-0.0739-0.1872-0.38680.074-0.233-0.02090.029-0.07570.2884-0.00890.0220.1103-0.03370.0479-10.5035-5.93166.5794
51.3357-0.08290.82922.5918-0.58780.6286-0.1105-0.0925-0.09550.36150.21030.1583-0.1373-0.1172-0.09980.27950.03260.03480.12070.03280.018-21.1953-3.553547.8333
61.57850.52070.08741.0074-0.30650.4353-0.03830.1075-0.10420.0380.05960.0818-0.01750.1102-0.02140.1627-0.00830.01670.1708-0.03380.0405-11.4632-1.8022103.93
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-37 - 45
2X-RAY DIFFRACTION2B-39 - 46
3X-RAY DIFFRACTION3C-38 - 46
4X-RAY DIFFRACTION4D-39 - 45
5X-RAY DIFFRACTION5E-37 - 45
6X-RAY DIFFRACTION6F-38 - 46

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