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- PDB-3cvp: Structure of Peroxisomal Targeting Signal 1 (PTS1) binding domain... -

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Basic information

Entry
Database: PDB / ID: 3cvp
TitleStructure of Peroxisomal Targeting Signal 1 (PTS1) binding domain of Trypanosoma brucei Peroxin 5 (TbPEX5)complexed to PTS1 peptide (10-SKL)
Components
  • 10-SKL PTS1 peptide Ac-GTLSNRASKL
  • Peroxisome targeting signal 1 receptor PEX5
KeywordsTRANSPORT PROTEIN / TPR motifs / TPR protein / Peroxin 5 / PEX5 / PTS1 binding domain / Protein-peptide complex / Receptor / TPR repeat
Function / homology
Function and homology information


peroxisome matrix targeting signal-1 binding / protein import into peroxisome matrix, docking / peroxisomal membrane / metal ion binding / cytoplasm / cytosol
Similarity search - Function
PEX5/PEX5L / Tetratricopeptide repeat / Tetratricopeptide repeat domain / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Alpha
Similarity search - Domain/homology
Peroxisome targeting signal 1 receptor / Peroxisome targeting signal 1 receptor PEX5
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSampathkumar, P. / Roach, C. / Michels, P.A.M. / Hol, W.G.J.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Structural Insights into the recognition of peroxisomal targeting signal 1 by Trypanosoma brucei peroxin 5.
Authors: Sampathkumar, P. / Roach, C. / Michels, P.A. / Hol, W.G.
History
DepositionApr 18, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Aug 30, 2023Group: 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: Peroxisome targeting signal 1 receptor PEX5
B: 10-SKL PTS1 peptide Ac-GTLSNRASKL


Theoretical massNumber of molelcules
Total (without water)37,5942
Polymers37,5942
Non-polymers00
Water1,78399
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1020 Å2
ΔGint-2 kcal/mol
Surface area13100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.100, 66.277, 51.621
Angle α, β, γ (deg.)90.00, 104.70, 90.00
Int Tables number4
Space group name H-MP1211
DetailsTHE BIOLOGICAL UNIT OF PROTEIN PEX5 IS MONOMER

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Components

#1: Protein Peroxisome targeting signal 1 receptor PEX5


Mass: 36545.844 Da / Num. of mol.: 1
Fragment: Peroxisomal Targeting Singal 1 (PTS1) binding domain of TbPEX5
Mutation: K378A/E379A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Gene: PEX5 / Plasmid details: Derivative pET28 / Plasmid: pSKB3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9U7C3, UniProt: Q57W55*PLUS
#2: Protein/peptide 10-SKL PTS1 peptide Ac-GTLSNRASKL


Mass: 1048.196 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / 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 Å3/Da / Density % sol: 38.62 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 2.3M Potassium acetate, 0.1M sodium citrate monohydrate, pH 4.8 - 5.0, vapor diffusion, sitting drop, temperature 298K
PH range: 4.8 - 5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Aug 28, 2006 / Details: Osmic VariMax
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→32.95 Å / Num. all: 19960 / Num. obs: 19221 / % possible obs: 96.3 % / Observed criterion σ(I): 3 / Redundancy: 2.71 % / Biso Wilson estimate: 29.14 Å2 / Rsym value: 0.06 / Net I/σ(I): 11.1
Reflection shellResolution: 2→2.07 Å / Redundancy: 1.82 % / Mean I/σ(I) obs: 2.5 / Num. unique all: 1982 / Rsym value: 0.311 / % possible all: 79.1

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
CrystalCleardata collection
d*TREKdata reduction
d*TREKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB code 1FCH

1fch


Resolution: 2→32.95 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.915 / SU B: 4.834 / SU ML: 0.136 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.219 / ESU R Free: 0.188
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflectionSelection details
Rfree0.257 981 5.1 %RANDOM
Rwork0.212 ---
obs0.214 19217 96.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 34.05 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20.04 Å2
2---0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2→32.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2182 0 0 99 2281
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222229
X-RAY DIFFRACTIONr_angle_refined_deg1.0951.9433044
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1075283
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.24724.821112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.90415324
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4681513
X-RAY DIFFRACTIONr_chiral_restr0.0760.2339
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021760
X-RAY DIFFRACTIONr_nbd_refined0.2010.21061
X-RAY DIFFRACTIONr_nbtor_refined0.3020.21535
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.2116
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1720.256
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1570.26
X-RAY DIFFRACTIONr_mcbond_it0.6041.51452
X-RAY DIFFRACTIONr_mcangle_it1.05322251
X-RAY DIFFRACTIONr_scbond_it1.7493877
X-RAY DIFFRACTIONr_scangle_it2.8644.5792
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 67 -
Rwork0.269 1079 -
all-1146 -
obs--77.96 %

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