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- PDB-5ojj: Crystal structure of the Zn-bound ubiquitin-conjugating enzyme Ube2T -

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Basic information

Entry
Database: PDB / ID: 5ojj
TitleCrystal structure of the Zn-bound ubiquitin-conjugating enzyme Ube2T
ComponentsUbiquitin-conjugating enzyme E2 T
KeywordsLIGASE / Ubiquitin conjugating enzyme / zinc / domain swap / oligomer
Function / homology
Function and homology information


protein K29-linked ubiquitination / protein K27-linked ubiquitination / protein K6-linked ubiquitination / protein K11-linked ubiquitination / E2 ubiquitin-conjugating enzyme / protein monoubiquitination / ubiquitin conjugating enzyme activity / protein K63-linked ubiquitination / protein autoubiquitination / protein K48-linked ubiquitination ...protein K29-linked ubiquitination / protein K27-linked ubiquitination / protein K6-linked ubiquitination / protein K11-linked ubiquitination / E2 ubiquitin-conjugating enzyme / protein monoubiquitination / ubiquitin conjugating enzyme activity / protein K63-linked ubiquitination / protein autoubiquitination / protein K48-linked ubiquitination / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Fanconi Anemia Pathway / protein polyubiquitination / ubiquitin-protein transferase activity / DNA repair / ubiquitin protein ligase binding / DNA damage response / chromatin binding / nucleolus / nucleoplasm / ATP binding / nucleus
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
ACETATE ION / Ubiquitin-conjugating enzyme E2 T
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsMorreale, F.E. / Testa, A. / Chaugule, V.K. / Bortoluzzi, A. / Ciulli, A. / Walden, H.
CitationJournal: J. Med. Chem. / Year: 2017
Title: Mind the Metal: A Fragment Library-Derived Zinc Impurity Binds the E2 Ubiquitin-Conjugating Enzyme Ube2T and Induces Structural Rearrangements.
Authors: Morreale, F.E. / Testa, A. / Chaugule, V.K. / Bortoluzzi, A. / Ciulli, A. / Walden, H.
History
DepositionJul 21, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 4, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ubiquitin-conjugating enzyme E2 T
B: Ubiquitin-conjugating enzyme E2 T
C: Ubiquitin-conjugating enzyme E2 T
D: Ubiquitin-conjugating enzyme E2 T
E: Ubiquitin-conjugating enzyme E2 T
F: Ubiquitin-conjugating enzyme E2 T
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,24122
Polymers106,1196
Non-polymers1,12216
Water17,619978
1
A: Ubiquitin-conjugating enzyme E2 T
B: Ubiquitin-conjugating enzyme E2 T
C: Ubiquitin-conjugating enzyme E2 T
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,74212
Polymers53,0593
Non-polymers6839
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9640 Å2
ΔGint-139 kcal/mol
Surface area21780 Å2
MethodPISA
2
D: Ubiquitin-conjugating enzyme E2 T
E: Ubiquitin-conjugating enzyme E2 T
F: Ubiquitin-conjugating enzyme E2 T
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,49810
Polymers53,0593
Non-polymers4397
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9610 Å2
ΔGint-146 kcal/mol
Surface area21930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.020, 96.383, 89.996
Angle α, β, γ (deg.)90.00, 93.28, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Ubiquitin-conjugating enzyme E2 T / Cell proliferation-inducing gene 50 protein / E2 ubiquitin-conjugating enzyme T / Ubiquitin carrier ...Cell proliferation-inducing gene 50 protein / E2 ubiquitin-conjugating enzyme T / Ubiquitin carrier protein T / Ubiquitin-protein ligase T


Mass: 17686.469 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2T, HSPC150, PIG50 / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: Q9NPD8, E2 ubiquitin-conjugating enzyme
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 978 / 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: 2.29 Å3/Da / Density % sol: 46.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 10% PEG3350, 0.2 M calcium acetate, 0.1 M Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9282 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9282 Å / Relative weight: 1
ReflectionResolution: 1.85→48.75 Å / Num. obs: 81137 / % possible obs: 99.7 % / Redundancy: 3.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.038 / Net I/σ(I): 16.6
Reflection shellResolution: 1.85→1.89 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.292 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 4465 / CC1/2: 0.849 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YH2

1yh2


Resolution: 1.85→48.75 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.758 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.145 / ESU R Free: 0.123 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19885 4035 5 %RANDOM
Rwork0.17809 ---
obs0.17915 77077 99.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 28.966 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å2-0.24 Å2
2--0.7 Å20 Å2
3----0.73 Å2
Refinement stepCycle: 1 / Resolution: 1.85→48.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7215 0 48 978 8241
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0197484
X-RAY DIFFRACTIONr_bond_other_d0.0060.027218
X-RAY DIFFRACTIONr_angle_refined_deg1.4741.98610185
X-RAY DIFFRACTIONr_angle_other_deg0.965316712
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3725910
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.49623.982329
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.828151272
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0641554
X-RAY DIFFRACTIONr_chiral_restr0.0890.21104
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0218268
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021598
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_it1.7222.6683630
X-RAY DIFFRACTIONr_mcbond_other1.7182.6673628
X-RAY DIFFRACTIONr_mcangle_it2.6823.9844520
X-RAY DIFFRACTIONr_mcangle_other2.6833.9854521
X-RAY DIFFRACTIONr_scbond_it2.1712.9683854
X-RAY DIFFRACTIONr_scbond_other2.1712.9683855
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.5134.3275660
X-RAY DIFFRACTIONr_long_range_B_refined5.94122.6748796
X-RAY DIFFRACTIONr_long_range_B_other5.90822.5868721
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 262 -
Rwork0.236 5706 -
obs--99.55 %

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