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- PDB-5a4p: Structure of UBE2Z provides functional insight into specificity i... -

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Basic information

Entry
Database: PDB / ID: 5a4p
TitleStructure of UBE2Z provides functional insight into specificity in the FAT10 conjugation machinery
ComponentsUBIQUITIN-CONJUGATING ENZYME E2 Z
KeywordsLIGASE / E2 ENZYME / FAT10 CONJUGATION / UBIQUITIN CONJUGATION
Function / homology
Function and homology information


E2 ubiquitin-conjugating enzyme / cysteine-type endopeptidase inhibitor activity / ubiquitin conjugating enzyme activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin-dependent protein catabolic process / protein ubiquitination / positive regulation of apoptotic process / apoptotic process / negative regulation of apoptotic process ...E2 ubiquitin-conjugating enzyme / cysteine-type endopeptidase inhibitor activity / ubiquitin conjugating enzyme activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin-dependent protein catabolic process / protein ubiquitination / positive regulation of apoptotic process / apoptotic process / negative regulation of apoptotic process / nucleoplasm / ATP binding / nucleus / cytosol
Similarity search - Function
Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme/RWD-like
Similarity search - Domain/homology
MALONATE ION / DI(HYDROXYETHYL)ETHER / Ubiquitin-conjugating enzyme E2 Z
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSchelpe, J. / Monte, D. / Dewitte, F. / Sixma, T.K. / Rucktooa, P.
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Structure of Ube2Z Provides Functional Insight Into Specificity in the Fat10 Conjugation Machinery
Authors: Schelpe, J. / Monte, D. / Dewitte, F. / Sixma, T.K. / Rucktooa, P.
History
DepositionJun 11, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 18, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 25, 2015Group: Database references
Revision 1.2Jan 20, 2016Group: Database references
Revision 1.3Jan 10, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: UBIQUITIN-CONJUGATING ENZYME E2 Z
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9728
Polymers38,2491
Non-polymers7227
Water41423
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.309, 57.800, 105.090
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein UBIQUITIN-CONJUGATING ENZYME E2 Z / UBA6-SPECIFIC E2 CONJUGATING ENZYME 1 / USE1 / UBIQUITIN CARRIER PROTEIN Z / UBIQUITIN-PROTEIN ...UBA6-SPECIFIC E2 CONJUGATING ENZYME 1 / USE1 / UBIQUITIN CARRIER PROTEIN Z / UBIQUITIN-PROTEIN LIGASE Z / UBE2Z


Mass: 38249.082 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PETNKI-HIS-3C-LIC-KAN / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9H832, ubiquitin-protein ligase
#2: Chemical
ChemComp-MLI / MALONATE ION / Malonic acid


Mass: 102.046 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H2O4
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 1.79 Å3/Da / Density % sol: 31 % / Description: NONE
Crystal growDetails: 17% (W/V) PEG1500, 0.1M MMT PH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.03679
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 11, 2011 / Details: BENT MIRROR
RadiationMonochromator: SILICON CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03679 Å / Relative weight: 1
ReflectionResolution: 2.1→38.89 Å / Num. obs: 16612 / % possible obs: 94.3 % / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Biso Wilson estimate: 32.33 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 8
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 1.6 / % possible all: 95.2

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1X23

1x23


Resolution: 2.1→38.88 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.8777 / SU R Cruickshank DPI: 0.227 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.229 / SU Rfree Blow DPI: 0.197 / SU Rfree Cruickshank DPI: 0.198
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.2782 816 4.91 %RANDOM
Rwork0.2352 ---
obs0.2372 16612 99.25 %-
Displacement parametersBiso mean: 58.3 Å2
Baniso -1Baniso -2Baniso -3
1--12.9951 Å20 Å20 Å2
2--5.1972 Å20 Å2
3---7.7979 Å2
Refine analyzeLuzzati coordinate error obs: 0.425 Å
Refinement stepCycle: LAST / Resolution: 2.1→38.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1835 0 49 23 1907
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011936HARMONIC2
X-RAY DIFFRACTIONt_angle_deg12615HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d882SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes43HARMONIC2
X-RAY DIFFRACTIONt_gen_planes284HARMONIC5
X-RAY DIFFRACTIONt_it1936HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.94
X-RAY DIFFRACTIONt_other_torsion3.14
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion237SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2173SEMIHARMONIC4
LS refinement shellResolution: 2.1→2.25 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.3213 153 5.17 %
Rwork0.2575 2807 -
all0.2608 2960 -
obs--99.25 %
Refinement TLS params.Method: refined / Origin x: 18.1054 Å / Origin y: 22.8326 Å / Origin z: 121.425 Å
111213212223313233
T0.304 Å2-0.105 Å2-0.0341 Å2--0.304 Å20.0242 Å2---0.304 Å2
L0.9913 °2-1.0459 °2-0.5264 °2-2.9677 °2-0.1666 °2--3.0124 °2
S0.02 Å °0.0913 Å °0.174 Å °0.0638 Å °-0.0706 Å °-0.022 Å °0.096 Å °-0.1028 Å °0.0506 Å °
Refinement TLS groupSelection details: { A|* }

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