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- PDB-2v1r: Yeast Pex13 SH3 domain complexed with a peptide from Pex14 at 2.1... -

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Basic information

Entry
Database: PDB / ID: 2v1r
TitleYeast Pex13 SH3 domain complexed with a peptide from Pex14 at 2.1 A resolution
Components
  • PEROXISOMAL MEMBRANE PROTEIN PAS20
  • PEX14
KeywordsPROTEIN TRANSPORT / TRANSLOCATION / TRANSMEMBRANE / PEPTIDE COMPLEX / STRUCTURAL GENOMICS / PEROXISOME
Function / homology
Function and homology information


Class I peroxisomal membrane protein import / peroxisomal importomer complex / protein import into peroxisome matrix, docking / Peroxisomal protein import / E3 ubiquitin ligases ubiquitinate target proteins / transmembrane transporter complex / peroxisomal membrane / protein transmembrane transporter activity / protein-macromolecule adaptor activity / signaling receptor binding
Similarity search - Function
Peroxin 13, N-terminal / Peroxin 13 / Peroxin 13, N-terminal region / Peroxisome membrane anchor protein Pex14p, N-terminal / Peroxisomal membrane protein 14 / Pex14 N-terminal domain / SH3 Domains / SH3 domain / SH3 type barrels. / Src homology 3 domains ...Peroxin 13, N-terminal / Peroxin 13 / Peroxin 13, N-terminal region / Peroxisome membrane anchor protein Pex14p, N-terminal / Peroxisomal membrane protein 14 / Pex14 N-terminal domain / SH3 Domains / SH3 domain / SH3 type barrels. / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Roll / Winged helix-like DNA-binding domain superfamily / Mainly Beta
Similarity search - Domain/homology
Peroxisomal membrane protein PEX14 / Peroxisomal membrane protein PEX13
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsKursula, I. / Kursula, P. / Lehmann, F. / Zou, P. / Song, Y.H. / Wilmanns, M.
CitationJournal: To be Published
Title: Structural Genomics of Yeast SH3 Domains
Authors: Kursula, P. / Kursula, I. / Pinotsis, N. / Lehmann, F. / Zou, P. / Song, Y.H. / Wilmanns, M.
History
DepositionMay 29, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 3, 2008Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2013Group: Derived calculations / Other / Version format compliance
Revision 1.2Jul 24, 2019Group: Data collection / Derived calculations / Category: diffrn_source / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: PEROXISOMAL MEMBRANE PROTEIN PAS20
B: PEROXISOMAL MEMBRANE PROTEIN PAS20
P: PEX14
Q: PEX14
R: PEX14


Theoretical massNumber of molelcules
Total (without water)23,7995
Polymers23,7995
Non-polymers00
Water1,892105
1
A: PEROXISOMAL MEMBRANE PROTEIN PAS20
Q: PEX14
R: PEX14


Theoretical massNumber of molelcules
Total (without water)12,7613
Polymers12,7613
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2110 Å2
ΔGint-7.6 kcal/mol
Surface area7070 Å2
MethodPISA
2
B: PEROXISOMAL MEMBRANE PROTEIN PAS20
P: PEX14


Theoretical massNumber of molelcules
Total (without water)11,0392
Polymers11,0392
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area680 Å2
ΔGint-3.6 kcal/mol
Surface area6530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.440, 39.090, 39.140
Angle α, β, γ (deg.)86.85, 65.46, 62.04
Int Tables number1
Space group name H-MP1

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Components

#1: Protein PEROXISOMAL MEMBRANE PROTEIN PAS20 / PEROXIN-13 / PEX13


Mass: 9316.717 Da / Num. of mol.: 2 / Fragment: SH3 DOMAIN, RESIDUES 299-374
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P80667
#2: Protein/peptide PEX14


Mass: 1721.952 Da / Num. of mol.: 3 / Fragment: SH3 DOMAIN BINDING SEGMENT, RESIDUES 83-96 / Source method: obtained synthetically / Source: (synth.) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P53112
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 2.3 Å3/Da / Density % sol: 46.14 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.81
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.81 Å / Relative weight: 1
ReflectionResolution: 2.11→20 Å / Num. obs: 9925 / % possible obs: 93.7 % / Observed criterion σ(I): -3 / Redundancy: 2 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 9.5
Reflection shellResolution: 2.11→2.25 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 2.6 / % possible all: 87

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Processing

Software
NameClassification
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PHENIXrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1N5Z

1n5z


Resolution: 2.1→20 Å
RfactorNum. reflection% reflection
Rfree0.2286 463 5 %
Rwork0.1912 --
obs-9268 93.6 %
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1264 0 0 105 1369

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