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- PDB-2n87: Solution structure of the PPIase domain of TbPar42 -

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Basic information

Entry
Database: PDB / ID: 2n87
TitleSolution structure of the PPIase domain of TbPar42
ComponentsUncharacterized protein
KeywordsISOMERASE / PPIase domain / Parvulin
Function / homology
Function and homology information


maintenance of RNA location / protein serine/threonine phosphatase inhibitor activity / negative regulation of protein dephosphorylation / miRNA processing / peptidyl-prolyl cis-trans isomerase activity / mRNA splicing, via spliceosome / nuclear speck / mRNA binding / nucleus
Similarity search - Function
PPIC-type PPIASE domain / PpiC-type peptidyl-prolyl cis-trans isomerase family profile. / Peptidyl-prolyl cis-trans isomerase, PpiC-type / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / Chitinase A; domain 3 - #40 / FHA domain / Forkhead-associated (FHA) domain / SMAD/FHA domain superfamily / Chitinase A; domain 3 ...PPIC-type PPIASE domain / PpiC-type peptidyl-prolyl cis-trans isomerase family profile. / Peptidyl-prolyl cis-trans isomerase, PpiC-type / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / Chitinase A; domain 3 - #40 / FHA domain / Forkhead-associated (FHA) domain / SMAD/FHA domain superfamily / Chitinase A; domain 3 / Peptidyl-prolyl cis-trans isomerase domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Peptidyl-prolyl cis-trans isomerase
Similarity search - Component
Biological speciesTrypanosoma brucei brucei TREU927 (eukaryote)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing, molecular dynamics
Model detailslowest energy, model1
AuthorsRehic, E. / Bayer, P.
Citation
Journal: Biomolecules / Year: 2019
Title: Structural Analysis of the 42 kDa Parvulin of Trypanosoma brucei.
Authors: Rehic, E. / Hoenig, D. / Kamba, B.E. / Goehring, A. / Hofmann, E. / Gasper, R. / Matena, A. / Bayer, P.
#1: Journal: Febs Lett. / Year: 2010
Title: Functional characterization of two novel parvulins in Trypanosoma brucei.
Authors: Goh, J.Y. / Lai, C.Y. / Tan, L.C. / Yang, D. / He, C.Y. / Liou, Y.C.
#2: Journal: Biochim.Biophys.Acta / Year: 2010
Title: Identification of an atypical peptidyl-prolyl cis/trans isomerase from trypanosomatids.
Authors: Erben, E.D. / Valguarnera, E. / Nardelli, S. / Chung, J. / Daum, S. / Potenza, M. / Schenkman, S. / Tellez-Inon, M.T.
History
DepositionOct 5, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 12, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Nov 20, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_nmr_software
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _pdbx_nmr_software.name
SupersessionDec 2, 2020ID: 2MNT
Revision 1.3Dec 2, 2020Group: Advisory / Category: pdbx_database_PDB_obs_spr
Revision 1.4Aug 24, 2022Group: Database references / Category: citation / database_2
Item: _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)13,5221
Polymers13,5221
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 60structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Uncharacterized protein


Mass: 13522.224 Da / Num. of mol.: 1 / Fragment: residues 264-383
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei TREU927 (eukaryote)
Strain: 927/4 GUTat10.1 / Gene: Tb927.7.2480 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q57XM6

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1152D 1H-15N HSQC
1212D 1H-1H COSY
1312D 1H-1H TOCSY
1412D 1H-1H NOESY
1533D CBCA(CO)NH
1633D HN(CA)CB
1733D HNCA
1833D HN(CO)CA
1933D HNCO
11033D HN(CA)CO
11133D HBHA(CO)NH
11233D HNHAHB
11363D (H)CCH-TOCSY
11463D (H)CCH-COSY
11522D 1H-1H COSY
11622D 1H-1H TOCSY
11722D 1H-1H NOESY
11842D 1H-15N HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
150 mM potassium phosphate, 50 uM DSS, 500-550 uM protein, 90% H2O/10% D2O90% H2O/10% D2O
250 mM potassium phosphate, 50 uM DSS, 500-550 uM protein, 99.9% D2O99.9% D2O
350 mM potassium phosphate, 50 uM DSS, 500-550 uM [U-100% 13C; U-100% 15N] protein, 90% H2O/10% D2O90% H2O/10% D2O
450 mM potassium phosphate, 50 uM DSS, 500-550 uM [U-100% 15N] protein, 100% D2O100% D2O
550 mM potassium phosphate, 50 uM DSS, 500-550 uM [U-100% 15N] protein, 90% H2O/10% D2O90% H2O/10% D2O
650 mM potassium phosphate, 50 uM DSS, 500-550 uM [U-100% 13C] protein, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
50 mMpotassium phosphate-11
50 uMDSS-21
uMprotein-3500-5501
50 mMpotassium phosphate-42
50 uMDSS-52
uMprotein-6500-5502
50 mMpotassium phosphate-73
50 uMDSS-83
uMprotein-9[U-100% 13C; U-100% 15N]500-5503
50 mMpotassium phosphate-104
50 uMDSS-114
uMprotein-12[U-100% 15N]500-5504
50 mMpotassium phosphate-135
50 uMDSS-145
uMprotein-15[U-100% 15N]500-5505
50 mMpotassium phosphate-166
50 uMDSS-176
uMprotein-18[U-100% 13C]500-5506
Sample conditionspH: 6.26 / Temperature: 300 K

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NMR measurement

NMR spectrometerType: Bruker Avance Ultrashield / Manufacturer: Bruker / Model: Avance Ultrashield / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
CCPNCCPNpeak picking
CCPNCCPNchemical shift assignment
CCPNCCPNchemical shift calculation
CCPNCCPNdata analysis
TALOSDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
CYANA3Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics, simulated annealing, molecular dynamics
Software ordinal: 1
NMR constraintsNOE constraints total: 2268 / NOE intraresidue total count: 455 / NOE long range total count: 802 / NOE medium range total count: 443 / NOE sequential total count: 568 / Hydrogen bond constraints total count: 185 / Protein phi angle constraints total count: 103 / Protein psi angle constraints total count: 103
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 60 / Conformers submitted total number: 10

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