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- PDB-5mmc: Trypanosoma brucei Pex14 N-terminal domain -

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Basic information

Entry
Database: PDB / ID: 5mmc
TitleTrypanosoma brucei Pex14 N-terminal domain
ComponentsPeroxin 14
KeywordsSIGNALING PROTEIN / Peroxin 14 / Pex14 / Trypanosoma / peroxisome
Function / homology
Function and homology information


glycosome membrane / protein import into peroxisome matrix, docking / protein targeting to vacuole / glycosome / post-transcriptional regulation of gene expression
Similarity search - Function
Peroxisome membrane anchor protein Pex14p, N-terminal / Peroxisomal membrane protein 14 / Pex14 N-terminal domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Peroxisomal membrane protein PEX14
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodSOLUTION NMR / simulated annealing
AuthorsEmmanouilidis, L. / Tripsianes, K. / Sattler, M.
CitationJournal: Science / Year: 2017
Title: Inhibitors of PEX14 disrupt protein import into glycosomes and kill Trypanosoma parasites.
Authors: Dawidowski, M. / Emmanouilidis, L. / Kalel, V.C. / Tripsianes, K. / Schorpp, K. / Hadian, K. / Kaiser, M. / Maser, P. / Kolonko, M. / Tanghe, S. / Rodriguez, A. / Schliebs, W. / Erdmann, R. ...Authors: Dawidowski, M. / Emmanouilidis, L. / Kalel, V.C. / Tripsianes, K. / Schorpp, K. / Hadian, K. / Kaiser, M. / Maser, P. / Kolonko, M. / Tanghe, S. / Rodriguez, A. / Schliebs, W. / Erdmann, R. / Sattler, M. / Popowicz, G.M.
History
DepositionDec 9, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 8, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2017Group: Database references
Revision 1.2May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.3May 15, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peroxin 14


Theoretical massNumber of molelcules
Total (without water)8,0211
Polymers8,0211
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5050 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Peroxin 14


Mass: 8021.192 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Gene: PEX14 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8IEW2

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic13D (H)CCH-TOCSY
131isotropic13D HNCA
141isotropic13D HN(CA)CB
191isotropic13D CBCA(CO)NH
171isotropic23D 1H-15N NOESY
161isotropic23D 1H-13C NOESY
181isotropic23D 1H-13C NOESY aromatic

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Sample preparation

DetailsType: solution
Contents: 1 mM [U-99% 13C; U-99% 15N] Pex14, 90% H2O/10% D2O
Label: Sample1 / Solvent system: 90% H2O/10% D2O
SampleConc.: 1 mM / Component: Pex14 / Isotopic labeling: [U-99% 13C; U-99% 15N]
Sample conditionsIonic strength: 50 mM / Label: conditions1 / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE5001
Bruker AVANCEBrukerAVANCE9002

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Processing

NMR software
NameDeveloperClassification
CNSBrunger A. T. et.al.refinement
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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