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- PDB-1nm7: Solution structure of the ScPex13p SH3 domain -

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Basic information

Entry
Database: PDB / ID: 1nm7
TitleSolution structure of the ScPex13p SH3 domain
ComponentsPeroxisomal Membrane Protein PAS20
KeywordsPROTEIN TRANSPORT / Yeast / Membrane protein / Pex5p / Pex14p / Pex13p / import machine / SH3 domain
Function / homology
Function and homology information


Class I peroxisomal membrane protein import / peroxisomal importomer complex / protein import into peroxisome matrix, docking / Peroxisomal protein import / peroxisomal membrane / protein transmembrane transporter activity / protein-macromolecule adaptor activity
Similarity search - Function
Peroxin 13, N-terminal / Peroxin 13 / Peroxin 13, N-terminal region / SH3 Domains / SH3 domain / SH3 type barrels. / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain ...Peroxin 13, N-terminal / Peroxin 13 / Peroxin 13, N-terminal region / SH3 Domains / SH3 domain / SH3 type barrels. / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Roll / Mainly Beta
Similarity search - Domain/homology
Peroxisomal membrane protein PEX13
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / AMBIGUOUS DISTANCE RESTRAINTS SIMULATED ANNEALING WITH TORSION ANGLE DYNAMICS AS IMPLEMENTED IN ARIA1.0
AuthorsPires, J.R. / Hong, X. / Brockmann, C. / Volkmer-Engert, R. / Schneider-Mergener, J. / Oschkinat, H. / Erdmann, R.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: The ScPex13p SH3 Domain Exposes Two Distinct Binding Sites for Pex5p and Pex14p
Authors: Pires, J.R. / Hong, X. / Brockmann, C. / Volkmer-Engert, R. / Schneider-Mergener, J. / Oschkinat, H. / Erdmann, R.
History
DepositionJan 9, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 4, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peroxisomal Membrane Protein PAS20


Theoretical massNumber of molelcules
Total (without water)8,0861
Polymers8,0861
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Peroxisomal Membrane Protein PAS20 / Pex13p SH3 domain


Mass: 8086.208 Da / Num. of mol.: 1 / Fragment: SH3 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: pGEX-4T2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-DE3 / References: UniProt: P80667

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1223D 15N-separated NOESY
1332D NOESY
1442D NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.7mM [U-15N,13C] Pex13p SH3 domain, 20mM Phosphate Buffer, pH 6.0, 50mM NaCl100% D2O
20.7mM [U-15N] Pex13p SH3 domain, 20mM Phosphate Buffer, pH 6.0, 50mM NaCl90% H2O/10% D2O
30.7mM Unlabeled Pex13p SH3 domain, 20mM Phosphate Buffer, pH 6.0, 50mM NaCl90% H2O/10% D2O
40.7mM Unlabeled Pex13p SH3 domain, 20mM Phosphate Buffer, pH 6.0, 50mM NaCl100% D2O
Sample conditionsIonic strength: 50mM NaCl / pH: 6.0 / Pressure: 1 atm / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMRBrukerprocessing
Sparky3.106data analysis
ARIA1J.P.Linge, S.I.O'Donoghue, M.Nilgesstructure solution
CNS1structure solution
CNS1refinement
RefinementMethod: AMBIGUOUS DISTANCE RESTRAINTS SIMULATED ANNEALING WITH TORSION ANGLE DYNAMICS AS IMPLEMENTED IN ARIA1.0
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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