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- PDB-3cv0: Structure of Peroxisomal Targeting Signal 1 (PTS1) binding domain... -

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Basic information

Entry
Database: PDB / ID: 3cv0
TitleStructure of Peroxisomal Targeting Signal 1 (PTS1) binding domain of Trypanosoma brucei Peroxin 5 (TbPEX5)complexed to T. brucei Phosphoglucoisomerase (PGI) PTS1 peptide
Components
  • Peroxisome targeting signal 1 receptor PEX5
  • T. brucei PGI PTS1 peptide Ac-FNELSHL
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 / glucose-6-phosphate isomerase / glucose-6-phosphate isomerase activity / glucose 6-phosphate metabolic process / glycosome / carbohydrate derivative binding / monosaccharide binding / peroxisomal membrane / glycolytic process ...peroxisome matrix targeting signal-1 binding / protein import into peroxisome matrix, docking / glucose-6-phosphate isomerase / glucose-6-phosphate isomerase activity / glucose 6-phosphate metabolic process / glycosome / carbohydrate derivative binding / monosaccharide binding / peroxisomal membrane / glycolytic process / gluconeogenesis / metal ion binding / cytoplasm / cytosol
Similarity search - Function
PEX5/PEX5L / Phosphoglucose isomerase, C-terminal / Phosphoglucose isomerase signature 1. / Phosphoglucose isomerase (PGI) / Phosphoglucose isomerase, conserved site / Phosphoglucose isomerase, SIS domain 1 / Phosphoglucose isomerase, SIS domain 2 / Phosphoglucose isomerase / Phosphoglucose isomerase signature 2. / Glucose-6-phosphate isomerase family profile. ...PEX5/PEX5L / Phosphoglucose isomerase, C-terminal / Phosphoglucose isomerase signature 1. / Phosphoglucose isomerase (PGI) / Phosphoglucose isomerase, conserved site / Phosphoglucose isomerase, SIS domain 1 / Phosphoglucose isomerase, SIS domain 2 / Phosphoglucose isomerase / Phosphoglucose isomerase signature 2. / Glucose-6-phosphate isomerase family profile. / SIS domain superfamily / 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
Glucose-6-phosphate isomerase, glycosomal / 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 17, 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 / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.5Apr 3, 2024Group: Refinement description / Category: 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 PGI PTS1 peptide Ac-FNELSHL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,15114
Polymers37,4062
Non-polymers74512
Water2,090116
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.405, 66.404, 52.117
Angle α, β, γ (deg.)90.00, 104.47, 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: 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: a derivative pET28 / Plasmid: pSKB3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9U7C3, UniProt: Q57W55*PLUS
#2: Protein/peptide T. brucei PGI PTS1 peptide Ac-FNELSHL


Mass: 859.946 Da / Num. of mol.: 1 / Source method: obtained synthetically / References: UniProt: P13377
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsACE IS COVALENTLY BONDED TO PHE IN CHAIN B, BUT IS NOT OBSERVED IN ELECTRON DENSITY MAP

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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: 2.04 Å3/Da / Density % sol: 39.83 %
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: Dec 7, 2006 / Details: Osmic Varimax
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→43.96 Å / Num. all: 19875 / Num. obs: 19875 / % possible obs: 97.7 % / Redundancy: 3.49 % / Biso Wilson estimate: 25.2 Å2 / Rsym value: 0.105 / Net I/σ(I): 7.2
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.33 % / Mean I/σ(I) obs: 1.9 / Num. unique all: 2015 / Rsym value: 0.38 / % possible all: 81.1

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Processing

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

1fhc


Resolution: 2→40.19 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.921 / SU B: 4.642 / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.213 / ESU R Free: 0.178
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflectionSelection details
Rfree0.234 1013 5.1 %RANDOM
Rwork0.189 ---
obs0.192 19869 97.71 %-
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: 27.13 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å2-0.01 Å2
2--0.01 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.178 Å0.213 Å
Luzzati sigma a-0.13 Å
Refinement stepCycle: LAST / Resolution: 2→40.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2415 0 48 116 2579
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0212506
X-RAY DIFFRACTIONr_bond_other_d0.0160.021656
X-RAY DIFFRACTIONr_angle_refined_deg1.3271.9553393
X-RAY DIFFRACTIONr_angle_other_deg0.98934024
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7345315
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.63624.806129
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.08315390
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5331516
X-RAY DIFFRACTIONr_chiral_restr0.0810.2370
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022835
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02497
X-RAY DIFFRACTIONr_nbd_refined0.220.2588
X-RAY DIFFRACTIONr_nbd_other0.1850.21713
X-RAY DIFFRACTIONr_nbtor_refined0.1770.21209
X-RAY DIFFRACTIONr_nbtor_other0.0870.21224
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1790.2100
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2630.232
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2610.255
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1560.217
X-RAY DIFFRACTIONr_mcbond_it1.011.51983
X-RAY DIFFRACTIONr_mcbond_other0.1841.5615
X-RAY DIFFRACTIONr_mcangle_it1.15522458
X-RAY DIFFRACTIONr_scbond_it2.05231107
X-RAY DIFFRACTIONr_scangle_it2.9424.5928
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 54 -
Rwork0.273 1091 -
all-1145 -
obs-2015 78.86 %

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