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- PDB-5nl8: Pex4 of Hansenula Polymorpha -

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Basic information

Entry
Database: PDB / ID: 5nl8
TitlePex4 of Hansenula Polymorpha
ComponentsUbiquitin-conjugating enzyme E2-21 kDa
KeywordsTRANSFERASE / E3 Ligase / ligase
Function / homology
Function and homology information


peroxisome organization / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / ubiquitin-protein transferase activity / protein ubiquitination / ATP binding
Similarity search - Function
Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme/RWD-like / Roll / Alpha Beta
Similarity search - Domain/homology
Ubiquitin-conjugating enzyme E2-21 kDa
Similarity search - Component
Biological speciesPichia angusta (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsGroves, M. / Williams, C.
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2018
Title: Structural insights into K48-linked ubiquitin chain formation by the Pex4p-Pex22p complex.
Authors: Groves, M.R. / Schroer, C.F.E. / Middleton, A.J. / Lunev, S. / Danda, N. / Ali, A.M. / Marrink, S.J. / Williams, C.
History
DepositionApr 4, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 24, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ubiquitin-conjugating enzyme E2-21 kDa


Theoretical massNumber of molelcules
Total (without water)21,6721
Polymers21,6721
Non-polymers00
Water99155
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.350, 46.350, 206.410
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Ubiquitin-conjugating enzyme E2-21 kDa / E2 ubiquitin-conjugating enzyme PEX4 / Peroxin-4 / Ubiquitin carrier protein / Ubiquitin-protein ligase


Mass: 21671.980 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pichia angusta (fungus) / Gene: PEX4 / Plasmid: pETM30 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL
References: UniProt: O60015, E2 ubiquitin-conjugating enzyme
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 2.56 Å3/Da / Density % sol: 51.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1M MES pH 6.5 50% (v/v) PEG-200

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.03321 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 22, 2016
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03321 Å / Relative weight: 1
ReflectionResolution: 2.02→45.22 Å / Num. obs: 14409 / % possible obs: 92 % / Redundancy: 4.13 % / CC1/2: 0.995 / Rmerge(I) obs: 0.1469 / Net I/σ(I): 6.21
Reflection shellResolution: 2.02→2.093 Å / Redundancy: 1.63 % / Rmerge(I) obs: 1.014 / Mean I/σ(I) obs: 0.98 / Num. unique obs: 1206 / CC1/2: 0.426 / % possible all: 80

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Y9M

2y9m


Resolution: 2.2→45.22 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.78
RfactorNum. reflection% reflectionSelection details
Rfree0.262 584 5.01 %Random
Rwork0.2092 ---
obs0.2119 11654 95.06 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.2→45.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1479 0 0 55 1534
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041517
X-RAY DIFFRACTIONf_angle_d0.7962062
X-RAY DIFFRACTIONf_dihedral_angle_d14.577577
X-RAY DIFFRACTIONf_chiral_restr0.032230
X-RAY DIFFRACTIONf_plane_restr0.004261
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1999-2.42130.36351350.29022559X-RAY DIFFRACTION91
2.4213-2.77160.29391340.23662549X-RAY DIFFRACTION90
2.7716-3.49170.31361520.23272875X-RAY DIFFRACTION99
3.4917-45.23340.22051630.18263087X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 7.8065 Å / Origin y: -8.1476 Å / Origin z: -12.4062 Å
111213212223313233
T0.1879 Å20.0232 Å2-0.0069 Å2-0.3442 Å2-0.0149 Å2--0.2305 Å2
L2.5815 °2-0.2306 °2-0.5553 °2-1.2961 °20.8006 °2--2.2826 °2
S-0.084 Å °-0.3969 Å °0.0327 Å °0.0953 Å °0.0946 Å °0.0562 Å °-0.0026 Å °-0.0232 Å °0.0002 Å °
Refinement TLS groupSelection details: all

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