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

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Entry
Database: PDB / ID: 3cvl
TitleStructure of Peroxisomal Targeting Signal 1 (PTS1) binding domain of Trypanosoma brucei Peroxin 5 (TbPEX5)complexed to T. brucei Phosphofructokinase (PFK) PTS1 peptide
Components
  • Peroxisome targeting signal 1 receptor PEX5
  • T. brucei PFK PTS1 peptide Ac-HEELAKL
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 / 6-phosphofructokinase / protein import into peroxisome matrix, docking / 6-phosphofructokinase activity / glycosome / fructose 6-phosphate metabolic process / peroxisomal membrane / phosphate ion binding / glycolytic process / ATP binding ...peroxisome matrix targeting signal-1 binding / 6-phosphofructokinase / protein import into peroxisome matrix, docking / 6-phosphofructokinase activity / glycosome / fructose 6-phosphate metabolic process / peroxisomal membrane / phosphate ion binding / glycolytic process / ATP binding / metal ion binding / cytosol
Similarity search - Function
Pyrophosphate-dependent phosphofructokinase TP0108-type / : / PEX5/PEX5L / Phosphofructokinase domain / ATP-dependent 6-phosphofructokinase / Phosphofructokinase superfamily / Phosphofructokinase / Tetratricopeptide repeat / Tetratricopeptide repeat domain / TPR repeat region circular profile. ...Pyrophosphate-dependent phosphofructokinase TP0108-type / : / PEX5/PEX5L / Phosphofructokinase domain / ATP-dependent 6-phosphofructokinase / Phosphofructokinase superfamily / Phosphofructokinase / 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
ATP-dependent 6-phosphofructokinase / Peroxisome targeting signal 1 receptor PEX5
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.15 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: T. brucei PFK PTS1 peptide Ac-HEELAKL


Theoretical massNumber of molelcules
Total (without water)37,3872
Polymers37,3872
Non-polymers00
Water1,20767
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1100 Å2
ΔGint-3 kcal/mol
Surface area13380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.390, 66.360, 49.680
Angle α, β, γ (deg.)90.00, 105.13, 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: Binding domain,UNP residues 332-655 / 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
#2: Protein/peptide T. brucei PFK PTS1 peptide Ac-HEELAKL


Mass: 840.963 Da / Num. of mol.: 1 / Source method: obtained synthetically / References: UniProt: O15648
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 1.89 Å3/Da / Density % sol: 34.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.8
Details: 2.3M Potassium acetate, 0.1M sodium citrate monohydrate, pH 4.8, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Nov 15, 2006 / Details: Osmic VariMax optics
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.08→26.4 Å / Num. all: 16165 / Num. obs: 16165 / % possible obs: 97.6 % / Redundancy: 3.27 % / Biso Wilson estimate: 25.52 Å2 / Rsym value: 0.096 / Net I/σ(I): 6.5
Reflection shellResolution: 2.08→2.15 Å / Redundancy: 2.73 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.317 / % possible all: 85.4

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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: 2.15→26.17 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.912 / SU B: 7.911 / SU ML: 0.206 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.341 / ESU R Free: 0.253
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflectionSelection details
Rfree0.278 753 5.1 %RANDOM
Rwork0.212 ---
obs0.215 14844 97.36 %-
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: 23.242 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å2-0.01 Å2
2---0.03 Å20 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 2.15→26.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2332 0 0 67 2399
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222385
X-RAY DIFFRACTIONr_bond_other_d0.0010.021516
X-RAY DIFFRACTIONr_angle_refined_deg1.3681.9483261
X-RAY DIFFRACTIONr_angle_other_deg1.00833703
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7125307
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.18625.081124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.80215360
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1351514
X-RAY DIFFRACTIONr_chiral_restr0.080.2361
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022753
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02473
X-RAY DIFFRACTIONr_nbd_refined0.2220.2625
X-RAY DIFFRACTIONr_nbd_other0.1950.21597
X-RAY DIFFRACTIONr_nbtor_refined0.1850.21168
X-RAY DIFFRACTIONr_nbtor_other0.110.21216
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.283
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1470.231
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2380.264
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1550.210
X-RAY DIFFRACTIONr_mcbond_it0.9041.51926
X-RAY DIFFRACTIONr_mcbond_other0.1511.5598
X-RAY DIFFRACTIONr_mcangle_it1.07822396
X-RAY DIFFRACTIONr_scbond_it1.72531009
X-RAY DIFFRACTIONr_scangle_it2.5024.5859
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 46 -
Rwork0.245 1024 -
all-1070 -
obs--94.77 %

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