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- PDB-5yba: Dimeric Cyclophilin from T.vaginalis in complex with Myb1 peptide -

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Basic information

Entry
Database: PDB / ID: 5yba
TitleDimeric Cyclophilin from T.vaginalis in complex with Myb1 peptide
Components
  • Myb1 peptide
  • Peptidyl-prolyl cis-trans isomerase
KeywordsISOMERASE / Divergent loop cyclophilin / Cyclophilin A / Rotamase complex
Function / homology
Function and homology information


snRNA-activating protein complex / snRNA transcription by RNA polymerase III / RNA polymerase III type 3 promoter sequence-specific DNA binding / snRNA transcription by RNA polymerase II / cyclosporin A binding / peptidyl-prolyl cis-trans isomerase activity / RNA polymerase II CTD heptapeptide repeat P3 isomerase activity / RNA polymerase II CTD heptapeptide repeat P6 isomerase activity / peptidylprolyl isomerase / protein folding ...snRNA-activating protein complex / snRNA transcription by RNA polymerase III / RNA polymerase III type 3 promoter sequence-specific DNA binding / snRNA transcription by RNA polymerase II / cyclosporin A binding / peptidyl-prolyl cis-trans isomerase activity / RNA polymerase II CTD heptapeptide repeat P3 isomerase activity / RNA polymerase II CTD heptapeptide repeat P6 isomerase activity / peptidylprolyl isomerase / protein folding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / nucleus / cytoplasm
Similarity search - Function
: / Myb-like domain profile. / Myb-like DNA-binding domain / Myb-type HTH DNA-binding domain profile. / Cyclophilin-like / Cyclophilin / Myb domain / Cyclophilin-type peptidyl-prolyl cis-trans isomerase / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature. ...: / Myb-like domain profile. / Myb-like DNA-binding domain / Myb-type HTH DNA-binding domain profile. / Cyclophilin-like / Cyclophilin / Myb domain / Cyclophilin-type peptidyl-prolyl cis-trans isomerase / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain / Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD / Cyclophilin-like domain superfamily / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / Homeobox-like domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Peptidyl-prolyl cis-trans isomerase / MYB24
Similarity search - Component
Biological speciesTrichomonas vaginalis (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.062 Å
AuthorsCho, C.C. / Lin, M.H. / Martin, T. / Chou, C.C. / Chen, C. / Hsu, C.H.
CitationJournal: Sci Rep / Year: 2018
Title: Structural basis of interaction between dimeric cyclophilin 1 and Myb1 transcription factor in Trichomonas vaginalis
Authors: Martin, T. / Lou, Y.C. / Chou, C.C. / Wei, S.Y. / Sadotra, S. / Cho, C.C. / Lin, M.H. / Tai, J.H. / Hsu, C.H. / Chen, C.
History
DepositionSep 4, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 18, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 1, 2018Group: Data collection / Database references / Derived calculations
Category: citation_author / pdbx_struct_assembly ...citation_author / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _citation_author.identifier_ORCID
Revision 1.2Sep 12, 2018Group: Data collection / Database references / Category: pdbx_related_exp_data_set
Revision 1.3Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Myb1 peptide
A: Peptidyl-prolyl cis-trans isomerase
D: Myb1 peptide
C: Peptidyl-prolyl cis-trans isomerase


Theoretical massNumber of molelcules
Total (without water)40,7634
Polymers40,7634
Non-polymers00
Water2,900161
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, Size-exclusion chromatography with multi-angle light scattering, equilibrium centrifugation, Analytical ultra centrifugation- sedimentation velocity experiments also ...Evidence: light scattering, Size-exclusion chromatography with multi-angle light scattering, equilibrium centrifugation, Analytical ultra centrifugation- sedimentation velocity experiments also confirm dimeric nature of TvCyP1
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3450 Å2
ΔGint-15 kcal/mol
Surface area14580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.785, 78.071, 117.708
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein/peptide Myb1 peptide


Mass: 1023.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Minimum Binding Sequence of Myb1 / Source: (synth.) Trichomonas vaginalis (eukaryote) / References: UniProt: Q58HP2*PLUS
#2: Protein Peptidyl-prolyl cis-trans isomerase / PPIase


Mass: 19358.309 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: human parasite / Source: (gene. exp.) Trichomonas vaginalis (eukaryote) / Gene: TVAG_004440 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A2DT06, peptidylprolyl isomerase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 2.13 Å3/Da / Density % sol: 42.24 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 100 mM Tris-HCl pH 8.0, 30% (v/v) polyethylene glycol 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.9762 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.06→29.45 Å / Num. obs: 22285 / % possible obs: 91 % / Redundancy: 5.3 % / Net I/σ(I): 9.81
Reflection shellResolution: 2.06→2.13 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.543 / Mean I/σ(I) obs: 2.039 / Rsym value: 0.543 / % possible all: 90.3

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DYW

1dyw


Resolution: 2.062→29.448 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.08
RfactorNum. reflection% reflection
Rfree0.2129 2873 9.72 %
Rwork0.1679 --
obs0.1722 21926 71.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.062→29.448 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2777 0 0 161 2938
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072839
X-RAY DIFFRACTIONf_angle_d0.8953803
X-RAY DIFFRACTIONf_dihedral_angle_d16.8641685
X-RAY DIFFRACTIONf_chiral_restr0.057393
X-RAY DIFFRACTIONf_plane_restr0.005497
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0621-2.09590.2677660.2078625X-RAY DIFFRACTION34
2.0959-2.1320.3293660.222631X-RAY DIFFRACTION36
2.132-2.17080.2957750.189696X-RAY DIFFRACTION39
2.1708-2.21250.264870.1818773X-RAY DIFFRACTION43
2.2125-2.25770.2454860.1968796X-RAY DIFFRACTION46
2.2577-2.30670.2201990.1936902X-RAY DIFFRACTION51
2.3067-2.36040.25781060.19341023X-RAY DIFFRACTION55
2.3604-2.41940.2571100.2086984X-RAY DIFFRACTION57
2.4194-2.48480.22971150.1831119X-RAY DIFFRACTION62
2.4848-2.55780.24521300.20731171X-RAY DIFFRACTION66
2.5578-2.64040.2351320.19421247X-RAY DIFFRACTION71
2.6404-2.73470.22771460.17941359X-RAY DIFFRACTION76
2.7347-2.84410.21091590.16861476X-RAY DIFFRACTION83
2.8441-2.97340.2081800.17071601X-RAY DIFFRACTION89
2.9734-3.130.2411790.17221675X-RAY DIFFRACTION93
3.13-3.32580.18371810.1771741X-RAY DIFFRACTION97
3.3258-3.58220.21581890.16421747X-RAY DIFFRACTION99
3.5822-3.9420.18071900.14441801X-RAY DIFFRACTION100
3.942-4.51060.19031930.13661757X-RAY DIFFRACTION100
4.5106-5.67620.18851950.14861790X-RAY DIFFRACTION99
5.6762-29.45050.22931890.18311773X-RAY DIFFRACTION100

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