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- PDB-3ajb: Crystal Structure of human Pex3p in complex with N-terminal Pex19... -

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Basic information

Entry
Database: PDB / ID: 3ajb
TitleCrystal Structure of human Pex3p in complex with N-terminal Pex19p peptide
Components
  • Peroxisomal biogenesis factor 19
  • Peroxisomal biogenesis factor 3
KeywordsPROTEIN TRANSPORT / ALL ALPHA / Protein-Protein complex
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 / Class I peroxisomal membrane protein import / peroxisome organization ...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 / Class I peroxisomal membrane protein import / peroxisome organization / protein carrier chaperone / ABC transporters in lipid homeostasis / peroxisome fission / peroxisomal membrane / : / brush border membrane / peroxisome / ATPase binding / protein-macromolecule adaptor activity / protein stabilization / lipid binding / endoplasmic reticulum / protein-containing complex / nucleoplasm / nucleus / membrane / cytoplasm / cytosol
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 / Peroxisomal biogenesis factor 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsSato, Y. / Shibata, H. / Nakatsu, T. / Kato, H.
CitationJournal: Embo J. / Year: 2010
Title: Structural basis for docking of peroxisomal membrane protein carrier Pex19p onto its receptor Pex3p
Authors: Sato, Y. / Shibata, H. / Nakatsu, T. / Nakano, H. / Kashiwayama, Y. / Imanaka, T. / Kato, H.
History
DepositionMay 27, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 22, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 11, 2017Group: Refinement description / Category: software
Revision 1.3Mar 13, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peroxisomal biogenesis factor 3
B: Peroxisomal biogenesis factor 19


Theoretical massNumber of molelcules
Total (without water)41,8112
Polymers41,8112
Non-polymers00
Water88349
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1470 Å2
ΔGint-15 kcal/mol
Surface area14850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)147.600, 147.600, 86.202
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Peroxisomal biogenesis factor 3 / PEROXIN 3 / PEX3P


Mass: 36906.359 Da / Num. of mol.: 1 / Fragment: Cytosolic domain, UNP residues 49-373
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: hCG_18102, PEX3, TRG18 / Plasmid: PGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6FGP5, UniProt: P56589*PLUS
#2: Protein/peptide Peroxisomal biogenesis factor 19 / Peroxin 19 / PEX19P / Peroxisomal farnesylated protein / 33 kDa housekeeping protein


Mass: 4904.264 Da / Num. of mol.: 1 / Fragment: N-TERMINAL PEPTIDE, UNP residues 1-44 / Mutation: C8A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HK33, OK/SW-cl.22, PEX19, PXF / Plasmid: PGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P40855
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
13.2462.05
2
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 25% PEG 3350, 0.2M NaCl, 50mM MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1901
21002
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL41XU11
SYNCHROTRONSPring-8 BL38B120.9791, 0.9794, 0.9642
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDDec 6, 2007
RIGAKU JUPITER 2102CCDFeb 22, 2008
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Double-crystal monochromatorSINGLE WAVELENGTHMx-ray1
2MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.97911
30.97941
40.96421
ReflectionResolution: 2.5→50 Å / Num. all: 19774 / Num. obs: 19695 / % possible obs: 99.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 10.3 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 46.273
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 10.6 % / Rmerge(I) obs: 0.267 / % possible all: 99.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MAD / Resolution: 2.5→48.34 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.917 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 7.405 / SU ML: 0.168 / SU R Cruickshank DPI: 0.289 / Cross valid method: THROUGHOUT / ESU R: 0.292 / ESU R Free: 0.234 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25435 1001 5.1 %RANDOM
Rwork0.21923 ---
obs0.22095 18591 100 %-
all-19550 --
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: 50.555 Å2
Baniso -1Baniso -2Baniso -3
1-0.86 Å20.43 Å20 Å2
2--0.86 Å20 Å2
3----1.29 Å2
Refinement stepCycle: LAST / Resolution: 2.5→48.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2379 0 0 49 2428
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222417
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4611.9953295
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5445315
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.68824.75682
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.32915403
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5951510
X-RAY DIFFRACTIONr_chiral_restr0.0980.2416
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211744
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.7991.51599
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.57122583
X-RAY DIFFRACTIONr_scbond_it2.3383818
X-RAY DIFFRACTIONr_scangle_it3.9924.5712
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 79 -
Rwork0.246 1337 -
obs--100 %

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