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- PDB-7oxh: ttSlyD with pseudo-wild-type S2 peptide -

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Basic information

Entry
Database: PDB / ID: 7oxh
TitlettSlyD with pseudo-wild-type S2 peptide
Components
  • 30S ribosomal protein S2
  • Fragment of 30S ribosomal protein S2 peptide
  • Peptidyl-prolyl cis-trans isomerase
KeywordsISOMERASE / FKBP / chaperone
Function / homology
Function and homology information


peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / protein refolding / ribosomal small subunit assembly / cytosolic small ribosomal subunit / cytoplasmic translation / structural constituent of ribosome / zinc ion binding / metal ion binding / cytoplasm
Similarity search - Function
FKBP-type peptidyl-prolyl cis-trans isomerase / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / Peptidyl-prolyl cis-trans isomerase domain superfamily / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein S2 signature 2. / Ribosomal protein S2 signature 1. / Ribosomal protein S2, conserved site / Ribosomal protein S2 / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S2
Similarity search - Domain/homology
NICKEL (II) ION / DI(HYDROXYETHYL)ETHER / Small ribosomal subunit protein uS2 / Peptidyl-prolyl cis-trans isomerase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
Escherichia coli (E. coli)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsPazicky, S. / Lei, J. / Loew, C.
Funding support Germany, 2items
OrganizationGrant numberCountry
Joachim Herz Stiftung800026 Germany
German Federal Ministry for Education and Research05K18YEA Germany
CitationJournal: Cell.Mol.Life Sci. / Year: 2022
Title: Impact of distant peptide substrate residues on enzymatic activity of SlyD.
Authors: Pazicky, S. / Werle, A.A. / Lei, J. / Low, C. / Weininger, U.
History
DepositionJun 22, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 16, 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: Peptidyl-prolyl cis-trans isomerase
B: 30S ribosomal protein S2
E: Fragment of 30S ribosomal protein S2 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,68610
Polymers19,3643
Non-polymers1,3227
Water1,35175
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.225, 49.225, 131.214
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-201-

PE4

21A-327-

HOH

31A-353-

HOH

41A-363-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Peptidyl-prolyl cis-trans isomerase


Mass: 17400.234 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8) (bacteria)
Strain: ATCC 27634 / DSM 579 / HB8 / Gene: TTHA0346 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5SLE7, peptidylprolyl isomerase

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Protein/peptide , 2 types, 2 molecules BE

#2: Protein/peptide 30S ribosomal protein S2 / Small ribosomal subunit protein uS2


Mass: 1775.080 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (strain K12) (bacteria) / References: UniProt: P0A7V0
#3: Protein/peptide Fragment of 30S ribosomal protein S2 peptide


Mass: 188.225 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 5 types, 82 molecules

#4: Chemical ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000


Mass: 354.436 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C16H34O8 / Comment: precipitant*YM
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.4 Å3/Da / Density % sol: 48.67 %
Crystal growTemperature: 292.15 K / Method: counter-diffusion / pH: 6.5 / Details: Sodium cacodylate, PEG 200

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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: P14 (MX2) / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.7→42.63 Å / Num. obs: 20988 / % possible obs: 99.75 % / Redundancy: 14.3 % / Biso Wilson estimate: 33.64 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.03603 / Rpim(I) all: 0.01027 / Rrim(I) all: 0.03756 / Net I/σ(I): 37.59
Reflection shellResolution: 1.7→1.762 Å / Redundancy: 14.1 % / Rmerge(I) obs: 0.6969 / Mean I/σ(I) obs: 4.02 / Num. unique obs: 2046 / CC1/2: 0.93 / Rpim(I) all: 0.1894 / Rrim(I) all: 0.7229 / % possible all: 99.22

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PHASERphasing
Aimlessdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3cgm

3cgm


Resolution: 1.7→42.63 Å / SU ML: 0.1853 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.453
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.238 1020 4.86 %
Rwork0.2027 19959 -
obs0.2044 20979 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.83 Å2
Refinement stepCycle: LAST / Resolution: 1.7→42.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1287 0 46 75 1408
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00671364
X-RAY DIFFRACTIONf_angle_d0.96671836
X-RAY DIFFRACTIONf_chiral_restr0.0612193
X-RAY DIFFRACTIONf_plane_restr0.0068246
X-RAY DIFFRACTIONf_dihedral_angle_d11.1999197
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.790.28781300.26792770X-RAY DIFFRACTION99.45
1.79-1.90.27871670.22562800X-RAY DIFFRACTION99.9
1.9-2.050.25551470.21632810X-RAY DIFFRACTION99.9
2.05-2.260.23211330.20892829X-RAY DIFFRACTION99.93
2.26-2.580.27331420.2282853X-RAY DIFFRACTION99.97
2.58-3.250.2491490.22432881X-RAY DIFFRACTION100
3.25-42.630.21871520.18113016X-RAY DIFFRACTION99.22
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)
15.958149552111.13553637757-0.2902149571322.735786146860.5328779759761.672561798050.0248535432548-1.144467039680.2378338739920.100419214161-0.203198942120.493046918417-0.249974230743-0.717517676126-0.02003897851070.1501146654280.01296622158820.05968786877540.576160969245-0.03163986706050.24441258196830.115-16.84910.905
24.45249534183-1.12403759198-1.291995736730.5386193594550.1027245678090.0522675312565-0.204602425825-0.186123802879-0.6468208046570.04545611741890.02538767744510.12989276945-0.007130970328620.09077087049470.1108304189680.2113155105170.008799245529430.006181605404820.3805113851830.0004474021923140.28050586206818.405-18.3659.443
37.521667591130.2752710168080.7062058836013.09353672240.5940319742540.18038493548-0.4587034391150.9387900863613.34889052752-1.09025117556-0.4010440515461.48706678388-1.550047033270.00470909158630.172479778870.90184112455-0.201350150897-0.1402931850210.5126676517310.2509803003310.7882288763872.8982.2934.587
44.476511465220.08216624860660.1430178588371.97906528154-0.5582870643276.32601672499-0.6642081355740.274307088877-0.136923310772-0.1074216970230.130950822749-0.0699463733062-0.4831245891430.448167432876-0.1504177111510.449454871203-0.0702143511924-0.01659692745820.3567803067210.009695791486890.2667451420488.26-1.81219.013
52.935406650440.824014890774-1.260655871683.32483832078-0.4766977023912.78226135183-0.1421272558160.30939950235-0.315408150876-0.2218856634190.1951772981350.0554161085003-0.4670212442150.0490279669086-0.05975194724620.284847852851-0.0368801575948-0.0175062860640.445457293465-0.004070339243280.2362353891765.364-9.4727.972
64.013721021680.6735773827720.1804827440570.730812227894-0.5416079786660.5741416658680.0203014330357-1.231806561040.2673923263060.328400389177-0.2645460443050.313636567405-0.0876967830275-0.337150507610.0716697399250.2660612635450.007959217659480.07369784642730.699676760402-0.08800564932620.23663165488135.08-14.27416.358
76.15232608896-0.4059565455320.3753285004673.28876140698-0.4359438090920.388111210881-0.624753079567-1.546115526840.248827332179-0.461559346361-0.839280553715-0.230217389015-0.6414692222470.282243567382-0.1178533675680.8070816027840.0180025285154-0.07939398041011.14850758396-0.2412430038470.71896167847131.847-6.90216.076
88.57127051599-6.722887562511.487282360346.498841524840.5955902398712.52239009788-0.00639620234455-1.692012387771.158142813940.428717069811-0.3231078947821.71593094617-0.53482179967-0.0356947219516-0.1226330607580.443346875740.006580721251790.233360630551.09037323683-0.2584129066670.96564018004619.267-11.72513.489
91.999120077462.003175132342.001160597522.002451917342.001391325782.000784459431.495454721132.56910019449-1.60685163282-0.556729316014-2.022074601591.23990458687-0.745707875979-1.908083833430.8624919290380.5707100626170.24321169357-0.06325460920191.749205486030.316791494380.1563693449786.529-13.18416.741
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:44 )A1 - 44
2X-RAY DIFFRACTION2( CHAIN A AND RESID 45:78 )A45 - 78
3X-RAY DIFFRACTION3( CHAIN A AND RESID 79:89 )A79 - 89
4X-RAY DIFFRACTION4( CHAIN A AND RESID 90:99 )A90 - 99
5X-RAY DIFFRACTION5( CHAIN A AND RESID 100:125 )A100 - 125
6X-RAY DIFFRACTION6( CHAIN A AND RESID 126:145 )A126 - 145
7X-RAY DIFFRACTION7( CHAIN A AND RESID 146:155 )A146 - 155
8X-RAY DIFFRACTION8( CHAIN B AND RESID 5:15 )B5 - 15
9X-RAY DIFFRACTION9( CHAIN E AND RESID 1:2 )E1 - 2

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