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- PDB-7bff: Circular permutant of ribosomal protein S6, P54-55 truncated, I25... -

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Basic information

Entry
Database: PDB / ID: 7bff
TitleCircular permutant of ribosomal protein S6, P54-55 truncated, I25A 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: 1.66 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
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


Theoretical massNumber of molelcules
Total (without water)60,5376
Polymers60,5376
Non-polymers00
Water3,657203
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6670 Å2
ΔGint-3 kcal/mol
Surface area26390 Å2
Unit cell
Length a, b, c (Å)38.691, 68.070, 222.357
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: I25A
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.: 203 / 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: 2.42 Å3/Da / Density % sol: 49.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M sodium thiocyanate 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: 1.66→68.07 Å / Num. obs: 59779 / % possible obs: 83.8 % / Redundancy: 6.2 % / CC1/2: 0.994 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.032 / Rrim(I) all: 0.079 / Net I/σ(I): 12.9 / Num. measured all: 370499 / Scaling rejects: 156
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
1.66-1.696.70.8562341735150.8730.3580.9292.399.9
9.08-68.075.20.05727495310.9920.0270.06328.997.7

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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: 1.66→50.19 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.916 / SU B: 5.136 / SU ML: 0.081 / Cross valid method: FREE R-VALUE / σ(F): 0 / ESU R: 0.125 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2526 3081 5.2 %RANDOM
Rwork0.209 ---
obs0.2112 56610 83.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 79.23 Å2 / Biso mean: 28.263 Å2 / Biso min: 14.55 Å2
Baniso -1Baniso -2Baniso -3
1-1.89 Å20 Å20 Å2
2--1.6 Å20 Å2
3----3.49 Å2
Refinement stepCycle: final / Resolution: 1.66→50.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4183 0 0 203 4386
Biso mean---34.74 -
Num. residues----509
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0134237
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174024
X-RAY DIFFRACTIONr_angle_refined_deg1.981.6535730
X-RAY DIFFRACTIONr_angle_other_deg1.4911.5779259
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9065503
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.78221.096301
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.2115778
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9061558
X-RAY DIFFRACTIONr_chiral_restr0.0990.2515
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.024809
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02937
LS refinement shellResolution: 1.66→1.7 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.317 240 -
Rwork0.267 4972 -
obs--99.94 %
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)
10.5785-0.11680.22520.7289-0.060.8588-0.0664-0.018-0.0442-0.03380.09460.0178-0.01090.0567-0.02830.01210.00530.00350.07880.00790.1145-15.6785-10.509410.1535
20.5665-0.23080.26410.25040.10681.58260.0250.0769-0.00420.0148-0.02340.0309-0.11880.2445-0.00150.04920.0069-0.0060.0942-0.00550.107-9.7247-3.804229.5627
30.70710.6604-0.4751.0913-0.39951.052-0.011-0.0440.018-0.0736-0.00070.0564-0.01110.01220.01160.0126-0.0198-0.0030.0753-0.03670.1313-13.65224.908184.1049
40.19650.1950.25632.26161.02171.19290.019-0.0660.0065-0.1643-0.029-0.06250.1020.02830.010.09680.00280.00220.0452-0.00360.0899-9.2705-5.989766.4258
50.4389-0.1158-0.0231.5674-0.37290.6916-0.01010.0561-0.02080.11840.01090.0762-0.0068-0.0138-0.00080.08440.0114-0.00310.0106-0.01550.1152-20.657-2.890248.2312
61.41920.0961-0.02730.43710.06210.9823-0.05570.1722-0.08310.1130.03090.0554-0.05190.06850.02470.0486-0.0290.02760.0789-0.02930.1104-10.3764-1.6088104.0925
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-38 - 45
2X-RAY DIFFRACTION2B-39 - 46
3X-RAY DIFFRACTION3C-39 - 46
4X-RAY DIFFRACTION4D-38 - 46
5X-RAY DIFFRACTION5E-37 - 45
6X-RAY DIFFRACTION6F-38 - 46

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