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- PDB-1n5z: Complex structure of Pex13p SH3 domain with a peptide of Pex14p -

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Basic information

Entry
Database: PDB / ID: 1n5z
TitleComplex structure of Pex13p SH3 domain with a peptide of Pex14p
Components
  • 14-mer peptide from Peroxisomal membrane protein PEX14
  • Peroxisomal membrane protein PAS20
KeywordsPROTEIN TRANSPORT / SH3 domain / PxxP motif
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 / 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 / Src homology 3 domains / SH3 type barrels. ...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 / Src homology 3 domains / SH3 type barrels. / 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: 2.7 Å
AuthorsDouangamath, A. / Filipp, F.V. / Klein, A.T.J. / Barnett, P. / Zou, P. / Voorn-Brouwer, T. / Vega, M.C. / Mayans, O.M. / Sattler, M. / Distel, B. / Wilmanns, M.
CitationJournal: MOL.CELL / Year: 2002
Title: Topography for Independent Binding of alpha-Helical and PPII-Helical Ligands to a Peroxisomal SH3 Domain
Authors: Douangamath, A. / Filipp, F.V. / Klein, A.T.J. / Barnett, P. / Zou, P. / Voorn-Brouwer, T. / Vega, M.C. / Mayans, O.M. / Sattler, M. / Distel, B. / Wilmanns, M.
History
DepositionNov 8, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 11, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peroxisomal membrane protein PAS20
P: 14-mer peptide from Peroxisomal membrane protein PEX14
B: Peroxisomal membrane protein PAS20
Q: 14-mer peptide from Peroxisomal membrane protein PEX14


Theoretical massNumber of molelcules
Total (without water)24,9564
Polymers24,9564
Non-polymers00
Water32418
1
A: Peroxisomal membrane protein PAS20
P: 14-mer peptide from Peroxisomal membrane protein PEX14


Theoretical massNumber of molelcules
Total (without water)12,4782
Polymers12,4782
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1010 Å2
ΔGint-6 kcal/mol
Surface area5640 Å2
MethodPISA
2
B: Peroxisomal membrane protein PAS20
Q: 14-mer peptide from Peroxisomal membrane protein PEX14


Theoretical massNumber of molelcules
Total (without water)12,4782
Polymers12,4782
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1040 Å2
ΔGint-6 kcal/mol
Surface area5610 Å2
MethodPISA
3
A: Peroxisomal membrane protein PAS20
P: 14-mer peptide from Peroxisomal membrane protein PEX14

B: Peroxisomal membrane protein PAS20
Q: 14-mer peptide from Peroxisomal membrane protein PEX14


Theoretical massNumber of molelcules
Total (without water)24,9564
Polymers24,9564
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_455x-1/2,-y+1/2,-z1
Buried area3600 Å2
ΔGint-19 kcal/mol
Surface area9710 Å2
MethodPISA
4
A: Peroxisomal membrane protein PAS20
P: 14-mer peptide from Peroxisomal membrane protein PEX14

B: Peroxisomal membrane protein PAS20
Q: 14-mer peptide from Peroxisomal membrane protein PEX14


Theoretical massNumber of molelcules
Total (without water)24,9564
Polymers24,9564
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area2690 Å2
ΔGint-19 kcal/mol
Surface area10610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.350, 63.204, 66.935
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 Peroxisomal membrane protein PAS20 / Peroxin-13 / PEX13


Mass: 10782.284 Da / Num. of mol.: 2 / Fragment: SH3 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: pMALc2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P80667
#2: Protein/peptide 14-mer peptide from Peroxisomal membrane protein PEX14 / Peroxin-14


Mass: 1695.914 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: Chemically synthesized. This sequence occurs naturally in Saccharomyces cerevisiae.
References: UniProt: P53112
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 2.83 Å3/Da / Density % sol: 56.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.3
Details: Ammonium sulfate, lithium sulfate, tris, pH 7.3, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 22 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
11.25 mMPex13p(SH3)1drop
25 mMpeptide1drop
32.0 Mammonium sulfate1reservoir
4100 mMTris1reservoirpH7.3
5200 mMlithium sulfate1reservoir

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 1.1 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 10, 2001
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.7→25 Å / Num. all: 6298 / Num. obs: 5907 / % possible obs: 93.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 65 Å2 / Rsym value: 0.0065 / Net I/σ(I): 21.1
Reflection shellHighest resolution: 2.7 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 2.9 / Rsym value: 0.033 / % possible all: 97.4
Reflection
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 25 Å / Rmerge(I) obs: 0.065
Reflection shell
*PLUS
% possible obs: 97.4 % / Rmerge(I) obs: 0.33

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
BEASTmodel building
REFMAC5refinement
BEASTphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→25 Å / Cor.coef. Fo:Fc: 0.901 / Cor.coef. Fo:Fc free: 0.894 / SU B: 13.558 / SU ML: 0.278 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.36 / ESU R Free: 0.371 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27306 265 4.5 %RANDOM
Rwork0.24434 ---
all0.2456 6298 --
obs0.24568 5563 93.86 %-
Solvent computationShrinkage radii: 0.8 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 7.974 Å2
Baniso -1Baniso -2Baniso -3
1--1.3 Å20 Å20 Å2
2--2.31 Å20 Å2
3----1.01 Å2
Refinement stepCycle: LAST / Resolution: 2.7→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1326 0 0 18 1344
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0221329
X-RAY DIFFRACTIONr_angle_refined_deg1.7681.9661808
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.5483156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.7715243
X-RAY DIFFRACTIONr_chiral_restr0.0920.2189
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021034
X-RAY DIFFRACTIONr_nbd_refined0.280.3604
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.5131
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2690.353
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1820.56
X-RAY DIFFRACTIONr_mcbond_it0.871.5809
X-RAY DIFFRACTIONr_mcangle_it1.63121301
X-RAY DIFFRACTIONr_scbond_it2.1413520
X-RAY DIFFRACTIONr_scangle_it3.5064.5507
LS refinement shellResolution: 2.7→2.769 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.433 23
Rwork0.291 400
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.3703-0.383-1.29016.6867-0.31587.0682-0.00520.3273-0.2782-0.2535-0.1054-0.1954-0.0356-0.11280.11060.1065-0.0185-0.05120.0067-0.01030.1314-8.97614.82715.97
28.7024-0.5269-2.59215.7616-0.14498.0826-0.20520.5857-0.4655-0.03670.12270.03070.4923-0.29580.08240.1577-0.0082-0.00370.063-0.03710.123722.75130.619-0.169
329.5623-4.942914.251511.74742.120218.17470.9774-0.76340.1905-0.9687-0.67780.6756-0.0088-0.7528-0.29960.22410.0116-0.06550.2148-0.05850.1963-13.5321.62425.493
449.29389.573616.09339.459719.273112.8367-0.9187-2.29010.27860.80470.1106-2.2551.17141.35920.80810.25530.04910.03010.26940.00860.430926.27339.9387.728
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA7 - 777 - 77
2X-RAY DIFFRACTION2BC11 - 7911 - 79
3X-RAY DIFFRACTION3PB4 - 124 - 12
4X-RAY DIFFRACTION4QD4 - 124 - 12
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor Rfree: 0.308 / Rfactor Rwork: 0.234
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.007
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.31

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