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- PDB-4odk: Structure of SlyD from Thermus thermophilus in complex with T1 peptide -

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Basic information

Entry
Database: PDB / ID: 4odk
TitleStructure of SlyD from Thermus thermophilus in complex with T1 peptide
Components
  • Guanyl-specific ribonuclease T1
  • Peptidyl-prolyl cis-trans isomerase SlyD
KeywordsISOMERASE / CHAPERONE / FKBP domain / IF domain / peptidyl-prolyl isomerase / PPIase
Function / homology
Function and homology information


hyphal tip / ribonuclease T1 / ribonuclease T1 activity / cell septum / RNA endonuclease activity / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / protein refolding / lyase activity / RNA binding ...hyphal tip / ribonuclease T1 / ribonuclease T1 activity / cell septum / RNA endonuclease activity / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / protein refolding / lyase activity / RNA binding / metal ion binding / cytoplasm
Similarity search - Function
: / : / Guanine-specific ribonuclease N1/T1/U2 / Ribonuclease/ribotoxin / ribonuclease / 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. ...: / : / Guanine-specific ribonuclease N1/T1/U2 / Ribonuclease/ribotoxin / ribonuclease / 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 / Roll / Alpha Beta
Similarity search - Domain/homology
Guanyl-specific ribonuclease T1 / Peptidyl-prolyl cis-trans isomerase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
Aspergillus oryzae (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.401 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 27, 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: Guanyl-specific ribonuclease T1
C: Guanyl-specific ribonuclease T1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8934
Polymers20,8583
Non-polymers351
Water3,513195
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1830 Å2
ΔGint-19 kcal/mol
Surface area9670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.500, 52.990, 48.910
Angle α, β, γ (deg.)90.00, 111.18, 90.00
Int Tables number5
Space group name H-MC121

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Components

#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 Guanyl-specific ribonuclease T1 / RNase T1


Mass: 1728.798 Da / Num. of mol.: 2 / Fragment: T1 peptide (UNP residues 59-73) / Source method: obtained synthetically / Source: (synth.) Aspergillus oryzae (mold) / References: UniProt: P00651
#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.: 195 / 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: 2.53 Å3/Da / Density % sol: 51.47 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 13.2% PEG1500, 0.1 M HEPES, pH 7.5, 0.05 M sodium chloride, 11% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9191 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 3, 2013
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9191 Å / Relative weight: 1
ReflectionResolution: 1.4→29.1 Å / Num. all: 40188 / Num. obs: 40188 / % possible obs: 97.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Biso Wilson estimate: 23.11 Å2 / Rsym value: 0.023 / Net I/σ(I): 23.03
Reflection shellResolution: 1.4→1.44 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 2.02 / Num. unique all: 2832 / Rsym value: 0.714 / % possible all: 93.7

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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: 1.401→29.096 Å / SU ML: 0.13 / σ(F): 1.99 / Phase error: 19.03 / Stereochemistry target values: ML / Details: PDB ENTRY 3LUO
RfactorNum. reflection% reflectionSelection details
Rfree0.1671 1255 3.12 %RANDOM
Rwork0.1393 ---
obs0.1403 40188 97.79 %-
all-40188 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.401→29.096 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1288 0 1 195 1484
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051376
X-RAY DIFFRACTIONf_angle_d1.0271888
X-RAY DIFFRACTIONf_dihedral_angle_d12.692517
X-RAY DIFFRACTIONf_chiral_restr0.071202
X-RAY DIFFRACTIONf_plane_restr0.006258
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.401-1.45660.28331240.22064165X-RAY DIFFRACTION95
1.4566-1.52290.2031140.15854305X-RAY DIFFRACTION97
1.5229-1.60320.18721270.12034350X-RAY DIFFRACTION98
1.6032-1.70360.14691150.09784324X-RAY DIFFRACTION98
1.7036-1.83510.13711630.09524315X-RAY DIFFRACTION98
1.8351-2.01980.14311560.09484331X-RAY DIFFRACTION98
2.0198-2.31190.14831450.11244365X-RAY DIFFRACTION99
2.3119-2.91240.16641420.15844386X-RAY DIFFRACTION99
2.9124-29.10190.17481690.1524392X-RAY DIFFRACTION98

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