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- PDB-7oxk: ttSlyD with W4K pseudo-wild-type S2 peptide -

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Basic information

Entry
Database: PDB / ID: 7oxk
TitlettSlyD with W4K 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 / 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
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: 2.8 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)20,7493
Polymers20,7493
Non-polymers00
Water543
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3330 Å2
ΔGint-26 kcal/mol
Surface area9740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.365, 109.365, 93.641
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)
Symmetry operation#1: x,y,z
#2: x-y,x,z+2/3
#3: y,-x+y,z+1/3
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z
#9: y,x,-z+1/3
#10: -y,-x,-z+1/3
#11: -x+y,y,-z
#12: x,x-y,-z+2/3

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Components

#1: Protein Peptidyl-prolyl cis-trans isomerase


Mass: 17313.156 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 (bacteria) / References: UniProt: Q5SLE7, peptidylprolyl isomerase
#2: Protein/peptide 30S ribosomal protein S2 / Small ribosomal subunit protein uS2


Mass: 1718.050 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (strain K12) (bacteria) / References: UniProt: P0A7V0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O

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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: 3.9 Å3/Da / Density % sol: 68.49 %
Crystal growTemperature: 292.15 K / Method: microbatch / pH: 9 / Details: 1-4dioxane, bicine, PEG 20000

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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 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.8→47.36 Å / Num. obs: 8584 / % possible obs: 99.9 % / Redundancy: 18.4 % / Biso Wilson estimate: 101.85 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.0991 / Rpim(I) all: 0.0139 / Rrim(I) all: 0.05847 / Net I/σ(I): 19.68
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 19.1 % / Mean I/σ(I) obs: 0.95 / Num. unique obs: 822 / CC1/2: 0.316 / Rpim(I) all: 0.773 / Rrim(I) all: 3.416 / % possible all: 99.6

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Processing

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

4odl


Resolution: 2.8→47.36 Å / SU ML: 0.3771 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.0102
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2346 451 5.26 %
Rwork0.2174 8126 -
obs0.2185 8577 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 122.28 Å2
Refinement stepCycle: LAST / Resolution: 2.8→47.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1365 0 0 3 1368
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00631398
X-RAY DIFFRACTIONf_angle_d1.05081896
X-RAY DIFFRACTIONf_chiral_restr0.07203
X-RAY DIFFRACTIONf_plane_restr0.0044256
X-RAY DIFFRACTIONf_dihedral_angle_d5.5269184
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.90.3653450.3659822X-RAY DIFFRACTION99.6
3.2-4.040.24191510.24822662X-RAY DIFFRACTION100
4.04-47.360.21321460.19552843X-RAY DIFFRACTION99.87
Refinement TLS params.Method: refined / Origin x: 38.2065861067 Å / Origin y: 37.0267580723 Å / Origin z: 39.5885466028 Å
111213212223313233
T0.444414273013 Å20.169944426553 Å20.00039272733691 Å2-0.948070221865 Å2-0.0409700963939 Å2--0.681253332236 Å2
L2.02988175518 °2-1.99676856523 °20.67958069161 °2-7.29132169113 °2-4.0104297408 °2--6.53046738948 °2
S0.0453354268469 Å °-0.198142132206 Å °-0.267158702164 Å °-0.11442550008 Å °0.0261492241885 Å °-0.0877900280078 Å °0.687353111 Å °0.604771358814 Å °-0.0768991383481 Å °
Refinement TLS groupSelection details: all

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