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- PDB-4odl: Structure of SlyD from Thermus thermophilus in complex with S2 peptide -

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Basic information

Entry
Database: PDB / ID: 4odl
TitleStructure of SlyD from Thermus thermophilus in complex with S2 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 / 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
Chitinase A; domain 3 - #40 / Chitinase A; domain 3 / 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 ...Chitinase A; domain 3 - #40 / Chitinase A; domain 3 / 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 / 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: 2.916 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
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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 SlyD
B: Peptidyl-prolyl cis-trans isomerase SlyD
C: 30S ribosomal protein S2
D: 30S ribosomal protein S2
E: 30S ribosomal protein S2
F: 30S ribosomal protein S2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,3008
Polymers42,2296
Non-polymers712
Water1086
1
A: Peptidyl-prolyl cis-trans isomerase SlyD
D: 30S ribosomal protein S2
F: 30S ribosomal protein S2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1504
Polymers21,1153
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3570 Å2
ΔGint-38 kcal/mol
Surface area10470 Å2
MethodPISA
2
B: Peptidyl-prolyl cis-trans isomerase SlyD
C: 30S ribosomal protein S2
E: 30S ribosomal protein S2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1504
Polymers21,1153
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2810 Å2
ΔGint-32 kcal/mol
Surface area10310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.880, 110.880, 182.310
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

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Components

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


Mass: 17400.234 Da / Num. of mol.: 2
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: 1857.227 Da / Num. of mol.: 4 / Fragment: S2 peptide (UNP residues 20-34) / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli) / References: UniProt: P0A7V0
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.83 Å3/Da / Density % sol: 67.89 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 20% PEG3350, 0.1 M Bis-Tris, pH 5.5, 0.2 M ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 22, 2012
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.916→48.012 Å / Num. all: 14963 / Num. obs: 14963 / % possible obs: 99.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 8.4 % / Biso Wilson estimate: 84.82 Å2 / Rsym value: 0.047 / Net I/σ(I): 30.68
Reflection shellResolution: 2.916→2.99 Å / Redundancy: 8.5 % / Mean I/σ(I) obs: 3.27 / Num. unique all: 1071 / Rsym value: 0.679 / % possible all: 99.1

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.916→48.012 Å / SU ML: 0.36 / σ(F): 1.99 / Phase error: 23.68 / Stereochemistry target values: ML / Details: PDB ENTRY 3LUO
RfactorNum. reflection% reflectionSelection details
Rfree0.2244 753 5.04 %RANDOM
Rwork0.2103 ---
obs0.2109 14954 99.13 %-
all-14954 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.916→48.012 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2783 0 2 6 2791
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032859
X-RAY DIFFRACTIONf_angle_d0.7593886
X-RAY DIFFRACTIONf_dihedral_angle_d13.2281054
X-RAY DIFFRACTIONf_chiral_restr0.051409
X-RAY DIFFRACTIONf_plane_restr0.004525
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.916-3.14150.30421690.2662743X-RAY DIFFRACTION99
3.1415-3.45760.2281460.23792773X-RAY DIFFRACTION99
3.4576-3.95770.29991250.23122795X-RAY DIFFRACTION98
3.9577-4.98550.2081550.18282849X-RAY DIFFRACTION100
4.9855-48.01890.19361580.20363041X-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)
13.60460.46121.93631.2452-0.2612.2401-0.0477-0.44460.22140.2182-0.01-0.2521-0.21250.21680.03070.2623-0.08240.00170.6907-0.06620.322740.8883-41.487153.865
22.1352-2.0951-1.01472.83341.47831.83680.36220.3458-0.5012-0.7677-0.42540.2880.5611-0.12850.16820.94620.1383-0.03490.2615-0.04310.462259.2681-14.8639-23.473
30.0382-0.0681-0.04122.06960.440.10820.46350.447-0.24090.12080.2184-0.59740.27930.61730.00990.5330.07230.14131.1458-0.27910.629884.7084-18.3854-23.12
43.8476-0.1926-2.07243.33911.93432.13070.003-0.46080.41570.0316-0.06820.71531.6001-0.1618-0.0370.59890.0576-0.1560.7109-0.07330.339255.0623-57.875153.3148
51.54790.0298-0.47180.11650.35791.31840.05190.1986-0.1089-0.31850.1866-0.6053-0.07190.2551-0.20161.03890.50070.22230.3877-0.22590.486463.6281-9.6285-23.5784
60.6236-0.76731.20783.2664-2.35224.74630.1615-0.255-0.5171-0.1295-0.2035-0.5470.74720.3141-0.06480.3060.0128-0.0381.0438-0.13920.636939.979-47.545654.1295
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resseq 1:150)
2X-RAY DIFFRACTION2(chain 'B' and resseq 1:150)
3X-RAY DIFFRACTION3(chain 'C' and resseq 26:35)
4X-RAY DIFFRACTION4(chain 'D' and resseq 20:35)
5X-RAY DIFFRACTION5(chain 'E' and resseq 20:35)
6X-RAY DIFFRACTION6(chain 'F' and resseq 20:35)

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