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

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Basic information

Entry
Database: PDB / ID: 3cvq
TitleStructure of Peroxisomal Targeting Signal 1 (PTS1) binding domain of Trypanosoma brucei Peroxin 5 (TbPEX5)complexed to PTS1 peptide (7-SKL)
Components
  • PTS1 peptide 7-SKL (Ac-SNRWSKL)
  • 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.01 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: Advisory / Refinement description / Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Aug 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: PTS1 peptide 7-SKL (Ac-SNRWSKL)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5703
Polymers37,4782
Non-polymers921
Water21612
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
ΔGint-3 kcal/mol
Surface area14600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.794, 68.794, 230.232
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsTHE BIOLOGICAL UNIT OF PROTEIN PEX5 IS MONOMER

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Components

#1: Protein Peroxisome targeting signal 1 receptor PEX5


Mass: 36543.762 Da / Num. of mol.: 1 / Fragment: Binding domain,UNP residues 332-655 / Mutation: M411A/K415A
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 PTS1 peptide 7-SKL (Ac-SNRWSKL)


Mass: 934.051 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 3.64 Å3/Da / Density % sol: 66.19 %
Crystal growTemperature: 298 K / pH: 4.8
Details: 2.3M Potassium acetate, 0.1M sodium citrate monohydrate, pH 4.8 - 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 298KK, pH 4.80

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 7, 2006
RadiationMonochromator: DOUBLE CRYSTAL, SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 11776 / % possible obs: 99.9 % / Redundancy: 8 % / Biso Wilson estimate: 96.04 Å2 / Rsym value: 0.09 / Net I/σ(I): 22.7
Reflection shellResolution: 3→3.11 Å / Redundancy: 8.5 % / Mean I/σ(I) obs: 2.6 / Rsym value: 0.0704 / % possible all: 99.5

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB CODE 1FCH

1fch


Resolution: 3.01→47.62 Å / Cor.coef. Fo:Fc: 0.892 / Cor.coef. Fo:Fc free: 0.868 / SU B: 46.621 / SU ML: 0.402 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: TLS model / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.897 / ESU R Free: 0.446
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflectionSelection details
Rfree0.321 584 5 %RANDOM
Rwork0.273 ---
obs0.275 11705 99.7 %-
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: 97.12 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2--0.03 Å20 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 3.01→47.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2266 0 6 12 2284
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0212319
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4871.9443159
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.465291
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.32925.128117
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.44115337
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.1691512
X-RAY DIFFRACTIONr_chiral_restr0.1140.2349
X-RAY DIFFRACTIONr_gen_planes_refined0.0010.021825
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2310.2943
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.21540
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.252
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2850.222
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.140.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3561.51509
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.63922332
X-RAY DIFFRACTIONr_scbond_it0.9183924
X-RAY DIFFRACTIONr_scangle_it1.4884.5827
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.01→3.08 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.387 39 -
Rwork0.343 768 -
obs--96.76 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
18.4211-2.87775.26345.2381-0.78796.93250.37930.19710.29690.56920.66720.8674-1.2846-0.6861-1.04650.02060.17220.3324-0.23570.2058-0.1711-4.976525.565618.7519
29.4489-5.1324-4.02879.76512.84291.77910.3390.74420.2263-0.07241.24930.9425-0.8502-1.5549-1.5883-0.18280.00430.3267-0.22350.2357-0.3495-1.860327.07417.2888
30.76252.87-0.705913.015-6.42927.08570.5664-0.57720.28711.22270.30781.0854-0.7479-0.1983-0.8742-0.450.29920.1164-0.63590.0946-0.57764.897621.200516.1667
44.76311.12262.90940.6387-0.38724.85390.32030.37290.2644-0.1212-0.05430.2718-0.4316-0.0595-0.266-0.58260.1360.1288-0.65840.055-0.705814.754222.77328.7991
53.17270.74460.8864.44699.554526.9704-0.0030.47142.7270.26610.6843-1.635-0.54841.2897-0.6813-0.1124-0.05150.1909-0.34320.0643-0.259329.00932.47848.626
649.0865-21.9388-11.960310.51888.506816.92211.3476-4.30131.4501-0.31811.90810.34522.06182.5964-3.25570.23970.16960.22830.18360.1770.924332.344210.05772.7743
73.1090.756-2.73014.1785-2.19255.28720.52470.08890.07140.42120.1156-0.325-0.53360.423-0.6402-0.48390.0409-0.12-0.61220.0255-0.636626.573317.503617.7428
83.0473.6653-0.50937.0016-3.3572.99010.3169-0.63180.12580.6829-0.02510.0671-0.0521-0.0702-0.2918-0.35490.1083-0.0923-0.65820.0946-0.729211.01185.485926.8058
919.0639-17.17743.426145.4591-5.63416.14550.71030.32170.0077-1.3075-0.520.37710.9049-0.2772-0.1903-0.4022-0.119-0.1529-0.36760.1191-0.50631.5882-2.577619.1195
109.4816-0.1506-0.52735.948411.274221.3745-0.1654-0.1893-0.69361.01130.18870.78381.493-0.1158-0.02330.0395-0.2069-0.14640.05110.27560.1044-5.9096-2.793725.2438
118.5315.53717.94294.70576.87618.9046-0.318-1.2442-1.6541-3.90251.1478-1.8460.85080.2656-0.8298-0.06360.0536-0.0084-0.8281-0.0177-0.624614.92392.933516.0719
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A335 - 362
2X-RAY DIFFRACTION2A363 - 383
3X-RAY DIFFRACTION3A384 - 401
4X-RAY DIFFRACTION4A402 - 445
5X-RAY DIFFRACTION5A446 - 457
6X-RAY DIFFRACTION6A472 - 477
7X-RAY DIFFRACTION7A478 - 546
8X-RAY DIFFRACTION8A547 - 599
9X-RAY DIFFRACTION9A612 - 628
10X-RAY DIFFRACTION10A629 - 649
11X-RAY DIFFRACTION11B1 - 7

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