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- PDB-8cms: OTUB2 in covalent complex with LN5P45 -

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Basic information

Entry
Database: PDB / ID: 8cms
TitleOTUB2 in covalent complex with LN5P45
ComponentsUbiquitin thioesterase OTUB2
KeywordsHYDROLASE / Chemical modification / ubiquitin / deubiquitinase / inhibitor
Function / homology
Function and homology information


negative regulation of double-strand break repair / protein K11-linked deubiquitination / protein K48-linked deubiquitination / protein K63-linked deubiquitination / protein deubiquitination / ubiquitin binding / Ovarian tumor domain proteases / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / proteolysis / nucleus
Similarity search - Function
Ubiquitin thioesterase Otubain / Peptidase C65, otubain / Peptidase C65, otubain, subdomain 2 / Peptidase C65, otubain, subdomain 1 / Peptidase C65 Otubain / OTU domain / OTU domain profile. / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
Chem-V2X / Ubiquitin thioesterase OTUB2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsGan, J. / de Vries, J.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO)724.013.002 Netherlands
CitationJournal: Acs Chem.Biol. / Year: 2023
Title: Cellular Validation of a Chemically Improved Inhibitor Identifies Monoubiquitination on OTUB2.
Authors: Gan, J. / de Vries, J. / Akkermans, J.J.L.L. / Mohammed, Y. / Tjokrodirijo, R.T.N. / de Ru, A.H. / Kim, R.Q. / Vargas, D.A. / Pol, V. / Fasan, R. / van Veelen, P.A. / Neefjes, J. / van Dam, ...Authors: Gan, J. / de Vries, J. / Akkermans, J.J.L.L. / Mohammed, Y. / Tjokrodirijo, R.T.N. / de Ru, A.H. / Kim, R.Q. / Vargas, D.A. / Pol, V. / Fasan, R. / van Veelen, P.A. / Neefjes, J. / van Dam, H. / Ovaa, H. / Sapmaz, A. / Geurink, P.P.
History
DepositionFeb 21, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 15, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Ubiquitin thioesterase OTUB2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6372
Polymers27,4051
Non-polymers2321
Water1,15364
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry, Single compound bound to active site cysteine (confirmed with mutant)
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11620 Å2
Unit cell
Length a, b, c (Å)47.650, 45.250, 58.000
Angle α, β, γ (deg.)90.000, 96.050, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ubiquitin thioesterase OTUB2 / Deubiquitinating enzyme OTUB2 / OTU domain-containing ubiquitin aldehyde-binding protein 2 / ...Deubiquitinating enzyme OTUB2 / OTU domain-containing ubiquitin aldehyde-binding protein 2 / Otubain-2 / Ubiquitin-specific-processing protease OTUB2


Mass: 27405.096 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: OTUB2, C14orf137, OTB2, OTU2 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q96DC9, ubiquitinyl hydrolase 1
#2: Chemical ChemComp-V2X / (1~{S},2~{S})-~{N}'-ethanoyl-2-(3-methylphenyl)cyclopropane-1-carbohydrazide


Mass: 232.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H16N2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.27 Å3/Da / Density % sol: 45.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20 %v/v 2-Propanol 13 %w/v PEG 4K 0.1 M HEPES pH 8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Feb 16, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.77→47.43 Å / Num. obs: 24095 / % possible obs: 99.6 % / Redundancy: 3.2 % / CC1/2: 0.994 / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.077 / Rrim(I) all: 0.142 / Net I/σ(I): 7
Reflection shellResolution: 1.77→1.81 Å / Redundancy: 2.7 % / Rmerge(I) obs: 1.295 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 1360 / CC1/2: 0.338 / Rpim(I) all: 0.985 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.77→47.43 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.929 / SU B: 4.127 / SU ML: 0.12 / Cross valid method: FREE R-VALUE / ESU R: 0.136 / ESU R Free: 0.133
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2521 1229 5.103 %
Rwork0.2099 22853 -
all0.212 --
obs-24082 99.591 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 25.72 Å2
Baniso -1Baniso -2Baniso -3
1-0.805 Å20 Å2-0.657 Å2
2---0.279 Å2-0 Å2
3----0.378 Å2
Refinement stepCycle: LAST / Resolution: 1.77→47.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1857 0 17 64 1938
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0131924
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171761
X-RAY DIFFRACTIONr_angle_refined_deg1.6541.6362597
X-RAY DIFFRACTIONr_angle_other_deg1.4081.5864071
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9885227
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.26321.842114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.39615336
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg8.61151
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.981514
X-RAY DIFFRACTIONr_chiral_restr0.0810.2248
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022200
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02446
X-RAY DIFFRACTIONr_nbd_refined0.2180.2414
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1770.21668
X-RAY DIFFRACTIONr_nbtor_refined0.180.2941
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.2967
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.275
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1230.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3730.214
X-RAY DIFFRACTIONr_nbd_other0.2150.255
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2230.23
X-RAY DIFFRACTIONr_mcbond_it2.122.454908
X-RAY DIFFRACTIONr_mcbond_other2.1032.452907
X-RAY DIFFRACTIONr_mcangle_it3.1863.6751136
X-RAY DIFFRACTIONr_mcangle_other3.183.6741136
X-RAY DIFFRACTIONr_scbond_it3.3992.9661016
X-RAY DIFFRACTIONr_scbond_other3.3982.9681017
X-RAY DIFFRACTIONr_scangle_it5.374.2751458
X-RAY DIFFRACTIONr_scangle_other5.3684.2781459
X-RAY DIFFRACTIONr_lrange_it6.62829.1262159
X-RAY DIFFRACTIONr_lrange_other6.63329.1082153
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.77-1.8160.4880.3711694X-RAY DIFFRACTION99.6644
1.816-1.8660.354900.3311610X-RAY DIFFRACTION99.8238
1.866-1.920.309780.3031615X-RAY DIFFRACTION99.5297
1.92-1.9790.301990.291540X-RAY DIFFRACTION99.5143
1.979-2.0440.305810.2541479X-RAY DIFFRACTION99.7442
2.044-2.1150.266670.2391453X-RAY DIFFRACTION99.2815
2.115-2.1950.261780.2191393X-RAY DIFFRACTION99.8642
2.195-2.2840.24800.2091361X-RAY DIFFRACTION99.6542
2.284-2.3860.235730.1941296X-RAY DIFFRACTION99.7813
2.386-2.5020.27710.1971225X-RAY DIFFRACTION99.8459
2.502-2.6370.292570.181204X-RAY DIFFRACTION99.5264
2.637-2.7970.223620.2011094X-RAY DIFFRACTION99.7412
2.797-2.9890.288560.2021053X-RAY DIFFRACTION99.5512
2.989-3.2280.258500.219991X-RAY DIFFRACTION99.4269
3.228-3.5350.256540.202890X-RAY DIFFRACTION99.7886
3.535-3.9510.165510.173813X-RAY DIFFRACTION99.1963
3.951-4.5580.178350.155727X-RAY DIFFRACTION99.4778
4.558-5.5740.244230.174633X-RAY DIFFRACTION98.9442
5.574-7.8460.29240.232491X-RAY DIFFRACTION99.4209
7.846-47.430.284120.196291X-RAY DIFFRACTION99.0196

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