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- PDB-7oxi: ttSlyD with W4A pseudo-wild-type S2 peptide -

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Basic information

Entry
Database: PDB / ID: 7oxi
TitlettSlyD with W4A pseudo-wild-type S2 peptide
Components
  • 30S ribosomal protein S2
  • Peptidyl-prolyl cis-trans isomerase
KeywordsISOMERASE / FKBP / chaperone
Function / homology
Function and homology information


peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / ribosomal small subunit assembly / protein refolding / 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 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
Small ribosomal subunit protein uS2 / Peptidyl-prolyl cis-trans isomerase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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:
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Assembly

Deposited unit
A: Peptidyl-prolyl cis-trans isomerase
B: 30S ribosomal protein S2
C: 30S ribosomal protein S2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7564
Polymers20,7203
Non-polymers351
Water724
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3010 Å2
ΔGint-37 kcal/mol
Surface area10300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.862, 108.862, 91.061
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422
Space group name HallP642(x,y,z+1/6)

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Components

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


Mass: 1659.948 Da / Num. of mol.: 2 / Mutation: W23E, P25A, K28L, I30A / Source method: obtained synthetically / Source: (synth.) Escherichia coli (strain K12) (bacteria) / References: UniProt: P0A7V0
#3: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
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: 4.09 Å3/Da / Density % sol: 69.96 %
Crystal growTemperature: 292.15 K / Method: counter-diffusion / pH: 6.5 / Details: sodium cacodylate, MPD, PEG8000

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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: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.6→41.86 Å / Num. obs: 10215 / % possible obs: 99.9 % / Redundancy: 18.5 % / Biso Wilson estimate: 95.41 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.0567 / Rpim(I) all: 0.0139 / Rrim(I) all: 0.05847 / Net I/σ(I): 30.51
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 17.9 % / Rmerge(I) obs: 2.105 / Mean I/σ(I) obs: 1.43 / Num. unique obs: 988 / CC1/2: 0.704 / Rpim(I) all: 0.5057 / Rrim(I) all: 2.166 / % possible all: 99.4

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Processing

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

3cgm


Resolution: 2.6→41.86 Å / SU ML: 0.3141 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 37.9729
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2452 463 4.53 %
Rwork0.217 9750 -
obs0.2181 10213 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 119.85 Å2
Refinement stepCycle: LAST / Resolution: 2.6→41.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1357 0 1 4 1362
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01321390
X-RAY DIFFRACTIONf_angle_d1.85181888
X-RAY DIFFRACTIONf_chiral_restr0.1122203
X-RAY DIFFRACTIONf_plane_restr0.0124256
X-RAY DIFFRACTIONf_dihedral_angle_d6.4068184
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.70.3697400.3531985X-RAY DIFFRACTION99.4
2.98-3.760.29661510.27213211X-RAY DIFFRACTION100
3.76-41.860.22391740.19393380X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 16.4402406388 Å / Origin y: 57.0743859762 Å / Origin z: 38.7897743263 Å
111213212223313233
T0.546257780582 Å20.253760854532 Å20.0181180506183 Å2-0.835350530059 Å20.071983534737 Å2--0.634329526876 Å2
L2.23063085923 °2-1.79505143417 °2-0.772536020207 °2-4.20467557954 °22.34690642102 °2--4.91800652939 °2
S-0.0810547998793 Å °0.0393154294593 Å °0.219312716769 Å °0.0864143921312 Å °0.0321555315161 Å °0.211190102896 Å °-0.669997064838 Å °-0.798992753624 Å °-0.0114493924163 Å °
Refinement TLS groupSelection details: all

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