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- PDB-4bwf: Pex4p-Pex22p disulphide bond mutant -

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Basic information

Entry
Database: PDB / ID: 4bwf
TitlePex4p-Pex22p disulphide bond mutant
Components
  • PEROXISOME ASSEMBLY PROTEIN 22
  • UBIQUITIN-CONJUGATING ENZYME E2-21 KDA
KeywordsLIGASE/SIGNALING PROTEIN / LIGASE-SIGNALING PROTEIN COMPLEX / E2 COMPLEX / PEROXISOMAL PROTEIN / E2 CO-ACTIVATOR
Function / homology
Function and homology information


protein import into peroxisome matrix, receptor recycling / peroxisome organization / ubiquitin-protein transferase activator activity / positive regulation of protein autoubiquitination / peroxisomal membrane / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / protein monoubiquitination / protein autoubiquitination / positive regulation of protein ubiquitination ...protein import into peroxisome matrix, receptor recycling / peroxisome organization / ubiquitin-protein transferase activator activity / positive regulation of protein autoubiquitination / peroxisomal membrane / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / protein monoubiquitination / protein autoubiquitination / positive regulation of protein ubiquitination / protein polyubiquitination / ubiquitin-protein transferase activity / peroxisome / protein ubiquitination / ATP binding / nucleus / cytoplasm
Similarity search - Function
Peroxisome assembly protein 22 / Peroxisome assembly protein 22 / Peroxin 22, C-terminal domain superfamiliy / Peroxisomal biogenesis protein family / : / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2 ...Peroxisome assembly protein 22 / Peroxisome assembly protein 22 / Peroxin 22, C-terminal domain superfamiliy / Peroxisomal biogenesis protein family / : / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like / Roll / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Ubiquitin-conjugating enzyme E2-21 kDa / Peroxisome assembly protein 22
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.23 Å
AuthorsWilliams, C. / van den Berg, M. / Stanley, W.A. / Wilmanns, M. / Distel, B.
CitationJournal: Sci.Rep. / Year: 2013
Title: A Disulphide Bond in the E2 Enzyme Pex4P Modulates Ubiquitin-Conjugating Activity
Authors: Williams, C. / van den Berg, M. / Stanley, W.A. / Wilmanns, M. / Distel, B.
History
DepositionJul 1, 2013Deposition site: PDBE / Processing site: PDBE
SupersessionJul 17, 2013ID: 2Y9O
Revision 1.0Jul 17, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2013Group: Database references
Revision 1.2Dec 13, 2017Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Jul 17, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UBIQUITIN-CONJUGATING ENZYME E2-21 KDA
B: PEROXISOME ASSEMBLY PROTEIN 22
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3538
Polymers33,9812
Non-polymers3726
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2090 Å2
ΔGint-1.9 kcal/mol
Surface area14410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.858, 42.802, 60.540
Angle α, β, γ (deg.)90.00, 100.14, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein UBIQUITIN-CONJUGATING ENZYME E2-21 KDA / PEX4P / PEROXIN-4 / UBIQUITIN CARRIER PROTEIN / UBIQUITIN-PROTEIN LIGASE


Mass: 19541.334 Da / Num. of mol.: 1 / Fragment: UBC DOMAIN, RESIDUES 15-183 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Plasmid: PCW250 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): RIL / References: UniProt: P29340, ubiquitin-protein ligase
#2: Protein PEROXISOME ASSEMBLY PROTEIN 22 / PEX22P / PEROXIN-22


Mass: 14439.574 Da / Num. of mol.: 1 / Fragment: SOLUBLE DOMAIN, RESIDUES 54-180
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Plasmid: PCW218 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): RIL / References: UniProt: P39718
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUE 15 IS MUTATED FROM SERINE TO ALANINE TO AID CLONING. THE MUTATIONS CYSTEINE 105 & 146 TO ...RESIDUE 15 IS MUTATED FROM SERINE TO ALANINE TO AID CLONING. THE MUTATIONS CYSTEINE 105 & 146 TO SERINE WERE INTRODUCED TO TEST THE IMPORTANCE OF THE DISULPHIDE BOND. THE N-TERMINAL GLYCINE IS LEFT OVER FROM THE TAG THE N-TERMINAL GLYCINE AND ALANINE ARE LEFT OVER FROM THE TAG

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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: 2.53 Å3/Da / Density % sol: 51 % / Description: NONE
Crystal growpH: 7
Details: 8.0 % (V/V) ETHYLENE GLYCOL, 14.0 % (W/V) POLYETHYLENE GLYCOL, 0.1 M HEPES PH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.812
DetectorType: MARRESEARCH SX-165 / Detector: CCD / Date: Jul 21, 2010 / Details: SI 111
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.812 Å / Relative weight: 1
ReflectionResolution: 3.23→17.28 Å / Num. obs: 5612 / % possible obs: 96.9 % / Observed criterion σ(I): 2.5 / Redundancy: 2.3 % / Biso Wilson estimate: 79.765 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 3.5
Reflection shellResolution: 3.23→3.4 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 1.9 / % possible all: 97.9

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Y9M

2y9m


Resolution: 3.23→17.28 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.832 / SU B: 42.323 / SU ML: 0.32 / Cross valid method: THROUGHOUT / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.26384 252 4.5 %RANDOM
Rwork0.20269 ---
obs0.20546 5353 97.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.284 Å2
Baniso -1Baniso -2Baniso -3
1--1.67 Å20 Å24 Å2
2---0.79 Å20 Å2
3---2.46 Å2
Refinement stepCycle: LAST / Resolution: 3.23→17.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2183 0 24 7 2214
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0192257
X-RAY DIFFRACTIONr_bond_other_d0.0010.022134
X-RAY DIFFRACTIONr_angle_refined_deg0.9511.9673062
X-RAY DIFFRACTIONr_angle_other_deg0.69234925
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.165282
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.95624.94591
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.11815377
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.597159
X-RAY DIFFRACTIONr_chiral_restr0.0510.2353
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0212502
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02467
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.229→3.31 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.39 16 -
Rwork0.36 369 -
obs--94.13 %

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