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- PDB-2y9p: Pex4p-Pex22p mutant II structure -

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Basic information

Entry
Database: PDB / ID: 2y9p
TitlePex4p-Pex22p mutant II structure
Components
  • PEROXISOME ASSEMBLY PROTEIN 22
  • UBIQUITIN-CONJUGATING ENZYME E2-21 KDA
KeywordsLIGASE/TRANSPORT PROTEIN / LIGASE-TRANSPORT PROTEIN COMPLEX / E2 COMPLEX / ALPHA-BETA-ALPHA SANDWICH FOLD / 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: 3.25 Å
AuthorsWilliams, C. / van den Berg, M. / Panjikar, S. / Distel, B. / Wilmanns, M.
CitationJournal: To be Published
Title: Pex4P-Pex22P Structure
Authors: Williams, C. / van den Berg, M. / Panjikar, S. / Distel, B. / Wilmanns, M.
History
DepositionFeb 16, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 29, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2017Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)33,9702
Polymers33,9702
Non-polymers00
Water362
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint-9.1 kcal/mol
Surface area14070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.002, 41.630, 71.117
Angle α, β, γ (deg.)90.00, 98.46, 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: 19530.439 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: PCW232 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, SER 15 TO ALA ENGINEERED RESIDUE IN CHAIN A, ASN 156 TO ALA
Sequence detailsRESIDUE 15 IS MUTATED FROM SERINE TO ALANINE TO AID CLONING. RESIDUE ASPARAGINE 156 IS MUTATED TO ...RESIDUE 15 IS MUTATED FROM SERINE TO ALANINE TO AID CLONING. RESIDUE ASPARAGINE 156 IS MUTATED TO ALANINE TO TEST ITS EFFECT ON THE PEX22P INTERACTION. 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: 2.58 Å3/Da / Density % sol: 52.28 % / 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: ESRF / Beamline: ID23-1 / Wavelength: 0.978
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 13, 2010 / Details: SI (111)
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 3.25→47.54 Å / Num. obs: 5245 / % possible obs: 97 % / Observed criterion σ(I): 5 / Redundancy: 3.5 % / Biso Wilson estimate: 86.1 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 9.4
Reflection shellResolution: 3.25→3.42 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 4.4 / % possible all: 79.8

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTY 2Y9M

2y9m


Resolution: 3.25→47.54 Å / Cor.coef. Fo:Fc: 0.898 / Cor.coef. Fo:Fc free: 0.817 / SU B: 28.257 / SU ML: 0.48 / Cross valid method: THROUGHOUT / ESU R: 0.52 / ESU R Free: 0.591 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.26765 237 4.5 %RANDOM
Rwork0.20723 ---
obs0.20994 5005 96.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.638 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å20 Å2-0.05 Å2
2--0.3 Å20 Å2
3----0.17 Å2
Refinement stepCycle: LAST / Resolution: 3.25→47.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2202 0 0 2 2204
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222250
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2211.963065
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4445288
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.32624.65186
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.3615367
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.486159
X-RAY DIFFRACTIONr_chiral_restr0.0730.2357
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211673
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_it0.4751.51449
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.92322349
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.1983801
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.1084.5716
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: 3.245→3.329 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.245 15 -
Rwork0.254 228 -
obs--64.29 %

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