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- PDB-2y9m: Pex4p-Pex22p structure -

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Basic information

Entry
Database: PDB / ID: 2y9m
TitlePex4p-Pex22p structure
Components
  • PEROXISOME ASSEMBLY PROTEIN 22
  • UBIQUITIN-CONJUGATING ENZYME E2-21 KDA
KeywordsLIGASE/TRANSPORT PROTEIN / LIGASE-TRANSPORT PROTEIN COMPLEX / UBIQUITIN CONJUGATING ENZYME / E2 COMPLEX / PEROXISOMAL PROTEIN / 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 / MAD / Resolution: 2.6 Å
AuthorsWilliams, C. / van den Berg, M. / Panjikar, S. / Distel, B. / Wilmanns, M.
CitationJournal: Embo J. / Year: 2011
Title: Insights Into Ubiquitin-Conjugating Enzyme/ Co-Activator Interactions from the Structure of the Pex4P:Pex22P Complex.
Authors: Williams, C. / van den Berg, M. / Panjikar, S. / Stanley, W.A. / Distel, B. / Wilmanns, M.
History
DepositionFeb 15, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 26, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2011Group: Database references
Revision 1.2Dec 7, 2011Group: Database references
Revision 1.3Jan 25, 2012Group: Other
Revision 1.4Apr 18, 2012Group: Other
Revision 1.5Dec 13, 2017Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.6Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / 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 / _pdbx_entry_details.has_protein_modification / _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

Downloads & links

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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)34,2616
Polymers34,0132
Non-polymers2484
Water1629
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2120 Å2
ΔGint-1.4 kcal/mol
Surface area14300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.328, 43.194, 60.474
Angle α, β, γ (deg.)90.00, 100.62, 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: 19573.463 Da / Num. of mol.: 1 / Fragment: UBC DOMAIN, RESIDUES 15-183 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: DISULPHIDE BOND BETWEEN RESIDUES 105 AND 146
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Plasmid: PCW187 / 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.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, SER 15 TO ALA
Has protein modificationY
Sequence detailsRESIDUE 15 IS MUTATED FROM SERINE TO ALANINE TO AID CLONING. THE N-TERMINAL GLYCINE IS LEFT OVER ...RESIDUE 15 IS MUTATED FROM SERINE TO ALANINE TO AID CLONING. 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: 2.76 Å3/Da / Density % sol: 55.46 %
Description: A 4 WAVELENGTH MAD DATA SET WAS COLLECTED AND THE MODEL FROM THIS DATASET WAS USED AS MR MODEL FOR THE NATIVE DATASET
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: ID14-1 / Wavelength: 0.9334
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 20, 2008 / Details: DIAMOND 111
RadiationMonochromator: DIAMOND 111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 2.6→34.7 Å / Num. obs: 11039 / % possible obs: 99.4 % / Observed criterion σ(I): 3 / Redundancy: 7.5 % / Biso Wilson estimate: 52 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 26.7
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 4.8 / % possible all: 99.1

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Processing

Software
NameVersionClassification
XDSdata reduction
SCALAdata scaling
Auto-Rickshawphasing
autoSHARPphasing
REFMAC5.4.0069refinement
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 2.6→20 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.897 / SU B: 22.417 / SU ML: 0.228 / Cross valid method: THROUGHOUT / ESU R: 0.38 / ESU R Free: 0.321 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25924 564 5.1 %RANDOM
Rwork0.20479 ---
obs0.20751 10450 99.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.852 Å2
Baniso -1Baniso -2Baniso -3
1--0.27 Å20 Å2-0.24 Å2
2--0.17 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2227 0 16 9 2252
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222316
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3331.9683141
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1665288
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.84624.52695
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.40215411
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.8951512
X-RAY DIFFRACTIONr_chiral_restr0.090.2357
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211704
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_it0.6131.51433
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.1722342
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.7853881
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.8754.5793
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: 2.6→2.666 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 44 -
Rwork0.277 742 -
obs--98.62 %
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)
18.5627-13.3272-10.703620.742816.659313.37960.4241-0.30240.8957-0.0143-0.29020.5736-1.3256-1.1711-0.13380.167-0.01160.0180.2613-0.0210.1281-23.4953-28.3906-37.2317
22.32491.12882.32461.9456-0.15633.5058-0.13860.11810.0524-0.1908-0.0090.5071-0.0859-0.72150.14770.19550.0308-0.03490.3077-0.00230.324-34.0124-20.1915-21.0412
31.9920.68791.35071.04240.14913.52240.03760.1883-0.2118-0.0939-0.01190.16890.1895-0.0931-0.02580.21360.00920.02710.1744-0.00190.2418-21.4086-25.5542-15.7515
43.60850.2178-0.32091.85620.89723.1129-0.02390.0291-0.3556-0.08380.01630.58850.3683-0.32810.00760.2025-0.0032-0.02840.23410.01830.2391-16.7605-25.80631.3471
51.7213-0.68480.17230.43340.66313.34390.0674-0.06890.60890.12050.02430.1087-0.8135-0.1337-0.09160.3129-0.00060.16780.1306-0.03340.2796-5.4325-11.286717.4607
63.6909-1.4388-0.62084.16641.19861.9151-0.0557-0.5499-0.02070.68-0.00980.6636-0.076-0.43880.06550.18280.01960.08630.20350.01010.13-11.2535-17.830413.5267
71.69850.1901-1.51870.21010.85256.89580.0799-0.28850.18760.3038-0.00980.1278-0.03730.0003-0.07010.16510.02710.00310.17570.05080.18761.7403-20.824116.5776
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A14 - 19
2X-RAY DIFFRACTION2A20 - 52
3X-RAY DIFFRACTION3A53 - 139
4X-RAY DIFFRACTION4A140 - 179
5X-RAY DIFFRACTION5B57 - 80
6X-RAY DIFFRACTION6B81 - 138
7X-RAY DIFFRACTION7B139 - 180

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