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- PDB-7oxj: ttSlyD with M8A pseudo-wild-type S2 peptide -

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Basic information

Entry
Database: PDB / ID: 7oxj
TitlettSlyD with M8A pseudo-wild-type S2 peptide
Components
  • 30S ribosomal protein S2
  • Fragment of 30S ribosomal protein S2 peptide
  • Peptidyl-prolyl cis-trans isomeraseProlyl isomerase
KeywordsISOMERASE / FKBP / chaperone
Function / homology
Function and homology information


peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / ribosomal small subunit assembly / cytosolic small ribosomal subunit / cytoplasmic translation / protein refolding / structural constituent of ribosome / zinc ion binding / metal ion binding / cytoplasm
Similarity search - Function
FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase / 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 / TRIETHYLENE GLYCOL / 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: 1.85 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
D: 30S ribosomal protein S2
E: Fragment of 30S ribosomal protein S2 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9169
Polymers19,3033
Non-polymers6136
Water1,54986
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2200 Å2
ΔGint-21 kcal/mol
Surface area10070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.282, 49.282, 130.700
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-203-

PG4

21A-205-

MG

31A-337-

HOH

41A-353-

HOH

51A-371-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Peptidyl-prolyl cis-trans isomerase / Prolyl 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 DE

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


Mass: 1714.962 Da / Num. of mol.: 1 / Mutation: P6A, M8A, K9L, I11A / 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 , 6 types, 92 molecules

#4: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#8: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Cl
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 48.75 %
Crystal growTemperature: 292.15 K / Method: microbatch / 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: 1.85→42.68 Å / Num. obs: 16345 / % possible obs: 99.9 % / Redundancy: 14.6 % / Biso Wilson estimate: 38.36 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.0417 / Rpim(I) all: 0.01155 / Rrim(I) all: 0.04336 / Net I/σ(I): 32.99
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 15.1 % / Rmerge(I) obs: 1.04 / Num. unique obs: 1595 / CC1/2: 0.924 / Rpim(I) all: 0.2738 / Rrim(I) all: 1.076 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4odl

4odl


Resolution: 1.85→42.68 Å / SU ML: 0.2155 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 25.0465
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2244 817 5 %
Rwork0.1984 15519 -
obs0.1997 16336 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 58.94 Å2
Refinement stepCycle: LAST / Resolution: 1.85→42.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1267 0 36 86 1389
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00941329
X-RAY DIFFRACTIONf_angle_d1.11741794
X-RAY DIFFRACTIONf_chiral_restr0.0727191
X-RAY DIFFRACTIONf_plane_restr0.0078241
X-RAY DIFFRACTIONf_dihedral_angle_d15.225187
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.970.28831340.24292543X-RAY DIFFRACTION99.78
1.97-2.120.26781320.21282517X-RAY DIFFRACTION99.89
2.12-2.330.24911350.20812558X-RAY DIFFRACTION99.93
2.33-2.670.24861340.22632557X-RAY DIFFRACTION100
2.67-3.370.2621370.21512598X-RAY DIFFRACTION99.96
3.37-42.680.19291450.18012746X-RAY DIFFRACTION99.76
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)
12.910672934821.45716041088-1.271077353395.530986795972.750906674842.932958179711.872289574672.996291083781.35147012346-2.75261387523-1.58061134825-0.967946302358-2.79035363079-3.03319599885-1.047847964451.358000944040.5685377826320.529315356941.384254605640.3280191851441.09271879119-20.944598627412.6934608052-12.6612682743
22.00118318793-9.034826203841.999669143541.997698374352.000908924291.99936850483-1.57439256426-5.5520981178-1.047673372440.1998449795061.492451642920.472508884234-0.1546908200361.956904265650.4060021448781.161012586450.311912984491-0.152277012591.126757530870.01416194979980.632990623243-15.2022395935-0.931884911693-16.6946265604
33.44015046125-1.53975714303-0.4831163185335.81615159512-0.5774165024183.088064723310.2626747656380.215994795853-0.315545183435-0.842331084168-0.364600490916-0.2213781848150.588433025610.4086054414280.06842875777890.4595645187330.1661584560380.0462672792780.323170994644-0.02959132348590.410274649955-31.607739521617.9229155704-10.078129017
42.78778535046-0.201842889661-0.1127753502954.62668406284-0.4680161746863.76803495149-0.0382996517389-0.107825194650.00627493317370.444173934957-0.0542480353516-0.173502476474-0.6243361313670.4917179414240.1221013611460.4304235299880.00447022875432-0.05602426589130.239281809483-0.01162924821170.299804958914-10.03777490511.12056511968-10.0447421039
50.6167781432640.7495229893580.1228424725481.87629582034-0.8325668030391.06432441281-0.05401477338410.381654108616-0.199072691748-1.36943431385-0.827228854274-0.920833500380.6581668530731.168894308790.5493836148110.7842074482430.316251585750.264678649250.6014014488190.1085038708280.52260203277-27.260073414923.3637121698-15.9939495824
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'D' and (resid 6 through 12 )
2X-RAY DIFFRACTION2chain 'E' and (resid 1 through 2 )
3X-RAY DIFFRACTION3chain 'A' and (resid 1 through 57 )
4X-RAY DIFFRACTION4chain 'A' and (resid 58 through 125 )
5X-RAY DIFFRACTION5chain 'A' and (resid 126 through 156 )

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