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- PDB-5qiu: Covalent fragment group deposition -- Crystal Structure of OUTB2 ... -

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Basic information

Entry
Database: PDB / ID: 5qiu
TitleCovalent fragment group deposition -- Crystal Structure of OUTB2 in complex with PCM-0103011
ComponentsUbiquitin thioesterase OTUB2
Keywordshydrolase/hydrolase inhibitor / SGC - Diamond I04-1 fragment screening / XChemExplorer / PROTEASE OTUB2 / DEUBIQUITINATING ENZYME OTUB2 / hydrolase-hydrolase inhibitor complex
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, subdomain 2 / Peptidase C65 Otubain, subdomain 1 / Peptidase C65, otubain / Peptidase C65, otubain, subdomain 2 / Peptidase C65, otubain, subdomain 1 / Peptidase C65 Otubain / 3 helical TM bundles of succinate and fumarate reductases / OTU domain / OTU domain profile. ...Ubiquitin thioesterase Otubain / Peptidase C65 Otubain, subdomain 2 / Peptidase C65 Otubain, subdomain 1 / Peptidase C65, otubain / Peptidase C65, otubain, subdomain 2 / Peptidase C65, otubain, subdomain 1 / Peptidase C65 Otubain / 3 helical TM bundles of succinate and fumarate reductases / OTU domain / OTU domain profile. / Papain-like cysteine peptidase superfamily / Phosphorylase Kinase; domain 1 / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-J5M / Unknown ligand / Ubiquitin thioesterase OTUB2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 1.56 Å
AuthorsSethi, R. / Douangamath, A. / Resnick, E. / Bradley, A.R. / Collins, P. / Brandao-Neto, J. / Talon, R. / Krojer, T. / Bountra, C. / Arrowsmith, C.H. ...Sethi, R. / Douangamath, A. / Resnick, E. / Bradley, A.R. / Collins, P. / Brandao-Neto, J. / Talon, R. / Krojer, T. / Bountra, C. / Arrowsmith, C.H. / Edwards, A. / London, N. / von Delft, F.
CitationJournal: To Be Published
Title: Covalent fragment group deposition
Authors: Sethi, R. / Douangamath, A. / Resnick, E. / Bradley, A.R. / Collins, P. / Brandao-Neto, J. / Talon, R. / Krojer, T. / Bountra, C. / Arrowsmith, C.H. / Edwards, A. / London, N. / von Delft, F.
History
DepositionAug 10, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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 thioesterase OTUB2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6658
Polymers26,3621
Non-polymers3037
Water4,216234
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.444, 58.427, 50.140
Angle α, β, γ (deg.)90.000, 116.280, 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: 26362.008 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 (E. coli) / References: UniProt: Q96DC9, ubiquitinyl hydrolase 1
#2: Chemical ChemComp-J5M / N-{3-[3-(trifluoromethyl)phenyl]prop-2-yn-1-yl}acetamide


Mass: 241.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H10F3NO
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 5 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 234 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.36 Å3/Da / Density % sol: 47.96 % / Mosaicity: 0.12 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 16% PEG4K, 0.1M HEPES pH 7.0, 8% 2-propanol, 5 mM DTT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 1.56→29.21 Å / Num. obs: 34960 / % possible obs: 99.8 % / Redundancy: 3.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.049 / Rrim(I) all: 0.092 / Net I/σ(I): 9.9 / Num. measured all: 117970 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.56-1.63.40.702866325350.6460.4420.8321.598.9
6.98-29.213.50.02414434150.9990.0150.02941.598.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0230refinement
Aimless0.5.32data scaling
PDB_EXTRACT3.23data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1TFF

1tff


Resolution: 1.56→29.23 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.953 / SU B: 4.676 / SU ML: 0.072 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.088 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2106 1535 4.4 %RANDOM
Rwork0.1447 ---
obs0.1477 33393 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 91.86 Å2 / Biso mean: 21.006 Å2 / Biso min: 10.04 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å20.02 Å2
2---0.15 Å2-0 Å2
3---0.01 Å2
Refinement stepCycle: final / Resolution: 1.56→29.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1843 0 26 234 2103
Biso mean--38.17 34.72 -
Num. residues----225
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0141924
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171705
X-RAY DIFFRACTIONr_angle_refined_deg1.7731.6612598
X-RAY DIFFRACTIONr_angle_other_deg2.0331.6453991
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4015232
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.90221.77113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.32315336
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.5661514
X-RAY DIFFRACTIONr_chiral_restr0.190.2249
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022160
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02389
X-RAY DIFFRACTIONr_mcbond_it2.8841.756907
X-RAY DIFFRACTIONr_mcbond_other2.8371.753906
X-RAY DIFFRACTIONr_mcangle_it3.7322.6461137
X-RAY DIFFRACTIONr_rigid_bond_restr2.81133629
X-RAY DIFFRACTIONr_sphericity_free29.2475168
X-RAY DIFFRACTIONr_sphericity_bonded16.82253655
LS refinement shellResolution: 1.561→1.601 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 109 -
Rwork0.204 2455 -
all-2564 -
obs--99.42 %

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