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- PDB-4odn: Structure of SlyD from Thermus thermophilus in complex with S2-pl... -

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Basic information

Entry
Database: PDB / ID: 4odn
TitleStructure of SlyD from Thermus thermophilus in complex with S2-plus peptide
Components
  • 30S ribosomal protein S2
  • Peptidyl-prolyl cis-trans isomerase SlyD
KeywordsISOMERASE / CHAPERONE / FKBP domain / IF domain / peptidyl-prolyl isomerase / PPIase
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
Chitinase A; domain 3 - #40 / Chitinase A; domain 3 / 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 ...Chitinase A; domain 3 - #40 / Chitinase A; domain 3 / 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 / Roll / Alpha Beta
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: 1.598 Å
AuthorsQuistgaard, E.M. / Low, C. / Nordlund, P.
CitationJournal: BMC Biol. / Year: 2016
Title: Molecular insights into substrate recognition and catalytic mechanism of the chaperone and FKBP peptidyl-prolyl isomerase SlyD.
Authors: Quistgaard, E.M. / Weininger, U. / Ural-Blimke, Y. / Modig, K. / Nordlund, P. / Akke, M. / Low, C.
History
DepositionJan 10, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)19,91910
Polymers19,3532
Non-polymers5668
Water4,107228
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2950 Å2
ΔGint-90 kcal/mol
Surface area9570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.830, 40.550, 53.220
Angle α, β, γ (deg.)90.00, 91.24, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein Peptidyl-prolyl cis-trans isomerase SlyD / TtSlyD


Mass: 17400.234 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: TTHA0346 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SLE7, peptidylprolyl isomerase
#2: Protein/peptide 30S ribosomal protein S2


Mass: 1952.414 Da / Num. of mol.: 1 / Fragment: S2-plus peptide (UNP residues 26-41) / Mutation: I41Y / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli) / References: UniProt: P0A7V0

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Non-polymers , 5 types, 236 molecules

#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 228 / 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: 2.22 Å3/Da / Density % sol: 44.6 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 20% PEG6000, 0.1 M citric acid, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 11, 2013
RadiationMonochromator: single bounce Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.598→28.412 Å / Num. all: 22554 / Num. obs: 22554 / % possible obs: 99.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.7 % / Biso Wilson estimate: 15.67 Å2 / Rsym value: 0.097 / Net I/σ(I): 12.74
Reflection shellResolution: 1.598→1.64 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 2.29 / Num. unique all: 1639 / Rsym value: 0.772 / % possible all: 97.7

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.598→28.412 Å / SU ML: 0.2 / σ(F): 1.35 / Phase error: 22.08 / Stereochemistry target values: ML / Details: PDB ENTRY 3LUO
RfactorNum. reflection% reflectionSelection details
Rfree0.1983 727 3.22 %RANDOM
Rwork0.1765 ---
obs0.1772 22553 99.34 %-
all-22553 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.598→28.412 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1262 0 30 228 1520
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0171344
X-RAY DIFFRACTIONf_angle_d1.1771832
X-RAY DIFFRACTIONf_dihedral_angle_d12.537496
X-RAY DIFFRACTIONf_chiral_restr0.072195
X-RAY DIFFRACTIONf_plane_restr0.005247
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.598-1.72140.26421350.23744314X-RAY DIFFRACTION98
1.7214-1.89460.241510.19674331X-RAY DIFFRACTION100
1.8946-2.16870.22321580.17074344X-RAY DIFFRACTION100
2.1687-2.7320.20561450.17514361X-RAY DIFFRACTION99
2.732-28.41630.1621380.16464476X-RAY DIFFRACTION99
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)
10.0529-0.08550.01620.08670.08810.22720.0148-0.00010.04-0.02310.0072-0.01320.03250.001900.0741-0.00630.00450.07550.0030.0758.0575-9.917612.6284
2-0.0060.0053-0.00680.0037-0.00440.02990.0121-0.0252-0.14890.1196-0.00950.11420.1537-0.0529-0.00760.31710.0136-0.04480.14240.00890.2409-3.7575-23.7263-6.0477
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A'
2X-RAY DIFFRACTION2chain 'B'

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