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- PDB-3mk4: X-Ray structure of human PEX3 in complex with a PEX19 derived peptide -

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Basic information

Entry
Database: PDB / ID: 3mk4
TitleX-Ray structure of human PEX3 in complex with a PEX19 derived peptide
Components
  • Peroxisomal biogenesis factor 19
  • Peroxisomal biogenesis factor 3
KeywordsPROTEIN TRANSPORT / Membrane / Peroxisome
Function / homology
Function and homology information


peroxisome membrane biogenesis / peroxisome membrane class-1 targeting sequence binding / establishment of protein localization to peroxisome / negative regulation of lipid binding / protein-lipid complex / peroxisome membrane targeting sequence binding / protein import into peroxisome membrane / protein targeting to peroxisome / protein carrier chaperone / Class I peroxisomal membrane protein import ...peroxisome membrane biogenesis / peroxisome membrane class-1 targeting sequence binding / establishment of protein localization to peroxisome / negative regulation of lipid binding / protein-lipid complex / peroxisome membrane targeting sequence binding / protein import into peroxisome membrane / protein targeting to peroxisome / protein carrier chaperone / Class I peroxisomal membrane protein import / peroxisome organization / peroxisome fission / ABC transporters in lipid homeostasis / peroxisomal membrane / chaperone-mediated protein folding / brush border membrane / peroxisome / ATPase binding / protein-macromolecule adaptor activity / protein stabilization / lipid binding / endoplasmic reticulum / protein-containing complex / nucleoplasm / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
Peroxin-3 / Peroxin-3 / Pex19 protein / Pex19, C-terminal domain superfamily / Pex19 protein family
Similarity search - Domain/homology
Peroxisomal biogenesis factor 19 / Peroxisomal biogenesis factor 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42 Å
AuthorsSchmidt, F. / Treiber, N. / Dodt, G. / Stehle, T.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Insights into peroxisome function from the structure of PEX3 in complex with a soluble fragment of PEX19
Authors: Schmidt, F. / Treiber, N. / Zocher, G. / Bjelic, S. / Steinmetz, M.O. / Kalbacher, H. / Stehle, T. / Dodt, G.
History
DepositionApr 14, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 30, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 16, 2013Group: Derived calculations
Revision 1.3Feb 19, 2014Group: Database references
Revision 1.4Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
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: Peroxisomal biogenesis factor 3
B: Peroxisomal biogenesis factor 19


Theoretical massNumber of molelcules
Total (without water)39,8242
Polymers39,8242
Non-polymers00
Water1,20767
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1220 Å2
ΔGint-10 kcal/mol
Surface area15250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.470, 65.670, 61.580
Angle α, β, γ (deg.)90.00, 91.53, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Peroxisomal biogenesis factor 3 / Peroxin-3 / Peroxisomal assembly protein PEX3


Mass: 37513.883 Da / Num. of mol.: 1 / Fragment: Cytosolic domain, UNP residues 41-373 / Mutation: C235S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PEX3 / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / Strain (production host): K-12 / References: UniProt: P56589
#2: Protein/peptide Peroxisomal biogenesis factor 19 / Peroxin-19 / Peroxisomal farnesylated protein / 33 kDa housekeeping protein


Mass: 2310.491 Da / Num. of mol.: 1 / Fragment: PEX19Pep, UNP residues 14-33 / Source method: obtained synthetically / Details: Synthesized peptide / References: UniProt: P40855
#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: 1.95 Å3/Da / Density % sol: 37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 24% PEG 3350, 0.1M Bis-Tris, 0.2M NaCl, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 18, 2009 / Details: mirrors
RadiationMonochromator: DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.42→25 Å / Num. obs: 11779 / % possible obs: 99.7 % / Observed criterion σ(I): 3 / Redundancy: 3.7 % / Rmerge(I) obs: 0.108 / Net I/σ(I): 20.2
Reflection shellResolution: 2.42→2.48 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 3 / % possible all: 99.8

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Processing

Software
NameVersionClassification
MxCuBEdata collection
PHASERphasing
REFMAC5.5.0102refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: unrefined model of PEX3

Resolution: 2.42→24.97 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.935 / SU B: 19.09 / SU ML: 0.197 / Isotropic thermal model: TLS / Cross valid method: THROUGHOUT / ESU R: 0.623 / ESU R Free: 0.269 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23368 589 5 %RANDOM
Rwork0.19431 ---
obs0.19634 11190 100 %-
all-12726 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.488 Å2
Baniso -1Baniso -2Baniso -3
1-1.87 Å20 Å21.77 Å2
2--0.66 Å20 Å2
3----2.43 Å2
Refinement stepCycle: LAST / Resolution: 2.42→24.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2363 0 0 67 2430
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222403
X-RAY DIFFRACTIONr_bond_other_d0.0010.021591
X-RAY DIFFRACTIONr_angle_refined_deg1.0811.983254
X-RAY DIFFRACTIONr_angle_other_deg0.85333909
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0915298
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.67724.766107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.87215436
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5131515
X-RAY DIFFRACTIONr_chiral_restr0.0570.2395
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022611
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02447
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_it1.34441509
X-RAY DIFFRACTIONr_mcbond_other0.4794600
X-RAY DIFFRACTIONr_mcangle_it2.22242438
X-RAY DIFFRACTIONr_scbond_it2.9946894
X-RAY DIFFRACTIONr_scangle_it4.2366815
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.42→2.482 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 41 -
Rwork0.289 793 -
obs--100 %
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)
11.2488-0.8996-0.51372.41991.27952.0388-0.0747-0.0420.0150.13270.0769-0.03990.23390.1345-0.00210.1588-0.0225-0.01610.16620.0210.149920.9591.89150.274
21.3879-0.3643-1.31431.46061.43443.56470.01990.0296-0.0114-0.21360.03280.0225-0.1482-0.0531-0.05260.0977-0.0228-0.04330.04990.01840.073217.841-0.57141.533
36.1486-3.15242.707631.48821.140543.66080.15120.1395-0.0016-0.66610.4718-1.02530.88382.7356-0.6230.09230.06440.05090.3261-0.06940.073137.668-11.19518.947
40.6645-0.0413-0.3490.99870.62471.635-0.041-0.0263-0.0024-0.05850.0588-0.01460.10530.0081-0.01770.1865-0.033-0.02780.10120.00730.153218.880.93644.439
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A40 - 158
2X-RAY DIFFRACTION2A159 - 368
3X-RAY DIFFRACTION3B15 - 30
4X-RAY DIFFRACTION4A1 - 39
5X-RAY DIFFRACTION4A374 - 399
6X-RAY DIFFRACTION4B34 - 64

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