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- PDB-7z0i: human PEX13 SH3 domain -

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Basic information

Entry
Database: PDB / ID: 7z0i
Titlehuman PEX13 SH3 domain
ComponentsPeroxisomal membrane protein PEX13
KeywordsPROTEIN TRANSPORT
Function / homology
Function and homology information


microtubule-based peroxisome localization / protein import into peroxisome matrix, translocation / peroxisomal importomer complex / fatty acid alpha-oxidation / protein import into peroxisome matrix, docking / Class I peroxisomal membrane protein import / peroxisomal membrane / suckling behavior / cerebral cortex cell migration / protein transmembrane transporter activity ...microtubule-based peroxisome localization / protein import into peroxisome matrix, translocation / peroxisomal importomer complex / fatty acid alpha-oxidation / protein import into peroxisome matrix, docking / Class I peroxisomal membrane protein import / peroxisomal membrane / suckling behavior / cerebral cortex cell migration / protein transmembrane transporter activity / locomotory behavior / Peroxisomal protein import / neuron migration / cellular response to reactive oxygen species / peroxisome / E3 ubiquitin ligases ubiquitinate target proteins / membrane / cytosol
Similarity search - Function
Peroxin 13, N-terminal / Peroxin 13 / Peroxin 13, N-terminal region / Variant SH3 domain / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain
Similarity search - Domain/homology
Peroxisomal membrane protein PEX13
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsGaussmann, S. / Zak, K. / Sattler, M.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)FOR1905 Germany
CitationJournal: Biorxiv / Year: 2022
Title: Intramolecular autoinhibition of human PEX13 modulates peroxisomal import
Authors: Gaussmann, S. / Ott, J. / Zak, K.M. / Delhommel, F. / Popowicz, G.M. / Schliebs, W. / Erdmann, R. / Sattler, M.
History
DepositionFeb 23, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 8, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peroxisomal membrane protein PEX13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,5893
Polymers9,4621
Non-polymers1272
Water91951
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-22 kcal/mol
Surface area5300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.949, 43.949, 86.780
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41
Components on special symmetry positions
IDModelComponents
11A-551-

HOH

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Components

#1: Protein Peroxisomal membrane protein PEX13 / Peroxin-13


Mass: 9461.601 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PEX13 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q92968
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.36 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.01M Zinc chloride, 0.1M Sodium acetate, 20% w/v PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.999995 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 8, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999995 Å / Relative weight: 1
ReflectionResolution: 1.8→43.39 Å / Num. obs: 7660 / % possible obs: 99.9 % / Redundancy: 13.6 % / CC1/2: 1 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.034 / Rrim(I) all: 0.089 / Net I/σ(I): 19.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
9-43.39130.0316410.0130.03399.1
1.8-1.8413.41.4434620.7380.5881.55999.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimlessdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
MOLREPphasing
BUCCANEERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1wxu

1wxu


Resolution: 1.8→39.238 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.946 / WRfactor Rfree: 0.219 / WRfactor Rwork: 0.172 / SU B: 3.501 / SU ML: 0.105 / Average fsc free: 0.8961 / Average fsc work: 0.9082 / Cross valid method: THROUGHOUT / ESU R: 0.128 / ESU R Free: 0.128
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2292 387 5.059 %RANDOM
Rwork0.1817 7262 --
all0.184 ---
obs-7649 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 34.564 Å2
Baniso -1Baniso -2Baniso -3
1-1.568 Å20 Å2-0 Å2
2--1.568 Å2-0 Å2
3----3.137 Å2
Refinement stepCycle: LAST / Resolution: 1.8→39.238 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms608 0 5 51 664
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.013633
X-RAY DIFFRACTIONr_bond_other_d0.0010.015619
X-RAY DIFFRACTIONr_angle_refined_deg1.4981.638851
X-RAY DIFFRACTIONr_angle_other_deg1.2821.5951420
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.882579
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.7221.38936
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.49815114
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.799156
X-RAY DIFFRACTIONr_chiral_restr0.0620.278
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02721
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02151
X-RAY DIFFRACTIONr_nbd_refined0.180.2100
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1710.2538
X-RAY DIFFRACTIONr_nbtor_refined0.1580.2282
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.2321
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.226
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2010.213
X-RAY DIFFRACTIONr_nbd_other0.2540.238
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1470.214
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0740.22
X-RAY DIFFRACTIONr_mcbond_it2.6813.261316
X-RAY DIFFRACTIONr_mcbond_other2.6763.254315
X-RAY DIFFRACTIONr_mcangle_it3.8514.858395
X-RAY DIFFRACTIONr_mcangle_other3.8484.868396
X-RAY DIFFRACTIONr_scbond_it3.5613.78315
X-RAY DIFFRACTIONr_scbond_other3.5563.782316
X-RAY DIFFRACTIONr_scangle_it5.5255.431456
X-RAY DIFFRACTIONr_scangle_other5.5195.434457
X-RAY DIFFRACTIONr_lrange_it7.48837.495661
X-RAY DIFFRACTIONr_lrange_other7.48237.542662
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.8470.279200.306555X-RAY DIFFRACTION99.1379
1.847-1.8970.298320.252510X-RAY DIFFRACTION99.8158
1.897-1.9520.314210.23511X-RAY DIFFRACTION99.8124
1.952-2.0120.291190.213494X-RAY DIFFRACTION99.8055
2.012-2.0780.203330.187470X-RAY DIFFRACTION99.8016
2.078-2.1510.189270.186461X-RAY DIFFRACTION99.7955
2.151-2.2320.336330.176445X-RAY DIFFRACTION99.7912
2.232-2.3220.271260.181415X-RAY DIFFRACTION100
2.322-2.4250.247170.176423X-RAY DIFFRACTION99.7732
2.425-2.5430.225170.169393X-RAY DIFFRACTION100
2.543-2.680.266220.173374X-RAY DIFFRACTION100
2.68-2.8420.137170.176350X-RAY DIFFRACTION100
2.842-3.0380.227150.179338X-RAY DIFFRACTION100
3.038-3.280.275180.174314X-RAY DIFFRACTION100
3.28-3.5910.251200.175281X-RAY DIFFRACTION100
3.591-4.0110.20280.17263X-RAY DIFFRACTION100
4.011-4.6250.19680.162236X-RAY DIFFRACTION100
4.625-5.6480.215200.166184X-RAY DIFFRACTION100
5.648-7.9210.16760.196159X-RAY DIFFRACTION100
7.921-39.2380.20380.1786X-RAY DIFFRACTION98.9474

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