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- PDB-8os1: X-ray structure of the Peroxisomal Targeting Signal 1 (PTS1) of T... -

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Basic information

Entry
Database: PDB / ID: 8os1
TitleX-ray structure of the Peroxisomal Targeting Signal 1 (PTS1) of Trypanosoma Cruzi PEX5 in complex with the PTS1 peptide
Components
  • (Peroxisome targeting signal 1 ...) x 2
  • Peroxisomal targeting signal 1 (PTS1)
KeywordsTRANSPORT PROTEIN / TPR domain / Complex / Peroxisomal targeting signal 1 binding domain / cargo recognition protein
Function / homology
Function and homology information


peroxisome matrix targeting signal-1 binding / protein import into peroxisome matrix, docking / peroxisomal membrane / cytosol
Similarity search - Function
PEX5/PEX5L / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Peroxisome targeting signal 1 receptor
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsNapolitano, V. / Blat, A. / Popowicz, G.M. / Dubin, G.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
Accelerated Early staGe drug dIScovery (AEGIS)European Union
CitationJournal: Int.J.Biol.Macromol. / Year: 2024
Title: Structural dynamics of the TPR domain of the peroxisomal cargo receptor Pex5 in Trypanosoma.
Authors: Banasik, M. / Napolitano, V. / Blat, A. / Abdulkarim, K. / Plewka, J. / Czaplewski, C. / Gieldon, A. / Kozak, M. / Wladyka, B. / Popowicz, G. / Dubin, G.
History
DepositionApr 17, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 2, 2024Provider: repository / Type: Initial release
Revision 2.0Oct 16, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / citation / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_entry_details / pdbx_modification_feature / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_ref
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _citation.journal_volume / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_entity_src_syn.entity_id / _pdbx_entry_details.has_protein_modification / _pdbx_poly_seq_scheme.entity_id / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_special_symmetry.label_asym_id / _struct_ref.entity_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Peroxisome targeting signal 1 receptor
A: Peroxisome targeting signal 1 receptor
D: Peroxisomal targeting signal 1 (PTS1)
C: Peroxisomal targeting signal 1 (PTS1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,06121
Polymers73,9394
Non-polymers1,12217
Water5,188288
1
B: Peroxisome targeting signal 1 receptor
D: Peroxisomal targeting signal 1 (PTS1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,49611
Polymers36,9312
Non-polymers5659
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Peroxisome targeting signal 1 receptor
C: Peroxisomal targeting signal 1 (PTS1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,56410
Polymers37,0082
Non-polymers5578
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)129.331, 69.936, 71.106
Angle α, β, γ (deg.)90.00, 100.05, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-807-

TRS

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Components

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Peroxisome targeting signal 1 ... , 2 types, 2 molecules BA

#1: Protein Peroxisome targeting signal 1 receptor


Mass: 36292.742 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Gene: ECC02_006719 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7J6Y110
#2: Protein Peroxisome targeting signal 1 receptor


Mass: 36368.859 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Gene: ECC02_006719 / Production host: Escherichia coli (E. coli)

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Protein/peptide , 1 types, 2 molecules DC

#3: Protein/peptide Peroxisomal targeting signal 1 (PTS1)


Mass: 638.733 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Trypanosoma cruzi (eukaryote)

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Non-polymers , 5 types, 305 molecules

#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 288 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.15 Å3/Da / Density % sol: 42.73 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.2 M MgCl2, 0.1 M Tris pH 8.5 and 30% (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.1→48.22 Å / Num. obs: 35080 / % possible obs: 95.9 % / Redundancy: 2.8 % / CC1/2: 0.959 / Net I/σ(I): 3.7
Reflection shellResolution: 2.1→2.16 Å / Num. unique obs: 2248 / CC1/2: 0.539

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
AutoProcessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→48.22 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.898 / SU B: 7.096 / SU ML: 0.184 / Cross valid method: THROUGHOUT / ESU R: 0.271 / ESU R Free: 0.217 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25284 1657 4.7 %RANDOM
Rwork0.19262 ---
obs0.19544 33423 95.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.849 Å2
Baniso -1Baniso -2Baniso -3
1-0.47 Å2-0 Å20.2 Å2
2--0.19 Å20 Å2
3----0.68 Å2
Refinement stepCycle: 1 / Resolution: 2.1→48.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4804 0 84 288 5176
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0125062
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4291.6416851
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1345629
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.44622.63289
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.41115807
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9491536
X-RAY DIFFRACTIONr_chiral_restr0.1110.2636
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023963
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.432.8572493
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.5584.2673117
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.8073.2212567
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined7.38739.9187959
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 10075 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1B
2A
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 88 -
Rwork0.28 1911 -
obs--74.81 %

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