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- PDB-6dxt: Structure of USP5 zinc-finger ubiquitin binding domain co-crystal... -

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Basic information

Entry
Database: PDB / ID: 6dxt
TitleStructure of USP5 zinc-finger ubiquitin binding domain co-crystallized with 3-(5-phenyl-1,3,4-oxadiazol-2-yl)propanoate
ComponentsUbiquitin carboxyl-terminal hydrolase 5
KeywordsHYDROLASE / DEUBIQUITINASE / USP5 / UBIQUITIN / STRUCTURAL GENOMICS CONSORTIUM / SGC
Function / homology
Function and homology information


protein K48-linked deubiquitination / negative regulation of ubiquitin-dependent protein catabolic process / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / ubiquitin binding / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / lysosome / protein ubiquitination / Ub-specific processing proteases ...protein K48-linked deubiquitination / negative regulation of ubiquitin-dependent protein catabolic process / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / ubiquitin binding / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / lysosome / protein ubiquitination / Ub-specific processing proteases / cysteine-type endopeptidase activity / proteolysis / zinc ion binding / nucleus / cytosol
Similarity search - Function
Ubiquitin carboxyl-terminal hydrolase 5, UBA1 domain / Ubiquitinyl hydrolase / Ubiquitinyl hydrolase, variant UBP zinc finger / Variant UBP zinc finger / Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger / Zinc finger, UBP-type / Zn-finger in ubiquitin-hydrolases and other protein / Zinc finger UBP-type profile. / UBA/TS-N domain / Ubiquitin specific protease (USP) domain signature 2. ...Ubiquitin carboxyl-terminal hydrolase 5, UBA1 domain / Ubiquitinyl hydrolase / Ubiquitinyl hydrolase, variant UBP zinc finger / Variant UBP zinc finger / Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger / Zinc finger, UBP-type / Zn-finger in ubiquitin-hydrolases and other protein / Zinc finger UBP-type profile. / UBA/TS-N domain / Ubiquitin specific protease (USP) domain signature 2. / Ubiquitin specific protease (USP) domain signature 1. / Ubiquitin specific protease, conserved site / Ubiquitin associated domain / Peptidase C19, ubiquitin carboxyl-terminal hydrolase / Ubiquitin carboxyl-terminal hydrolase / Ubiquitin specific protease domain / Ubiquitin specific protease (USP) domain profile. / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Papain-like cysteine peptidase superfamily / Zinc finger, RING/FYVE/PHD-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
3-(5-phenyl-1,3,4-oxadiazol-2-yl)propanoic acid / Ubiquitin carboxyl-terminal hydrolase 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsMann, M.K. / Harding, R.J. / Ravichandran, M. / Ferreira de Freitas, R. / Franzoni, I. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.M. / Schapira, M. / Structural Genomics Consortium (SGC)
CitationJournal: J.Med.Chem. / Year: 2019
Title: Discovery of Small Molecule Antagonists of the USP5 Zinc Finger Ubiquitin-Binding Domain.
Authors: Mann, M.K. / Franzoni, I. / de Freitas, R.F. / Tempel, W. / Houliston, S. / Smith, L. / Vedadi, M. / Arrowsmith, C.H. / Harding, R.J. / Schapira, M.
History
DepositionJun 29, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 9, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 11, 2023Group: 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 carboxyl-terminal hydrolase 5
B: Ubiquitin carboxyl-terminal hydrolase 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6689
Polymers27,0702
Non-polymers5977
Water3,063170
1
A: Ubiquitin carboxyl-terminal hydrolase 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9435
Polymers13,5351
Non-polymers4084
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ubiquitin carboxyl-terminal hydrolase 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7254
Polymers13,5351
Non-polymers1903
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.090, 85.440, 59.740
Angle α, β, γ (deg.)90.000, 100.290, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Ubiquitin carboxyl-terminal hydrolase 5 / Deubiquitinating enzyme 5 / Isopeptidase T / Ubiquitin thioesterase 5 / Ubiquitin-specific- ...Deubiquitinating enzyme 5 / Isopeptidase T / Ubiquitin thioesterase 5 / Ubiquitin-specific-processing protease 5


Mass: 13535.199 Da / Num. of mol.: 2 / Fragment: UNP residues 171-290
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: USP5, ISOT / Plasmid: pET28-mhl / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) codon plus / References: UniProt: P45974, ubiquitinyl hydrolase 1

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Non-polymers , 5 types, 177 molecules

#2: Chemical ChemComp-HHY / 3-(5-phenyl-1,3,4-oxadiazol-2-yl)propanoic acid


Mass: 218.209 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C11H10N2O3
#3: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Mass: 62.068 Da / Num. of mol.: 2 / Source method: isolated from a natural source
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Zn
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 170 / 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: 2.83 Å3/Da / Density % sol: 56.59 % / Mosaicity: 0 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.5 M ammonium sulfate, 0.1 M bis-tris pH 7.0, 25% ethylene glycol (v/v), 1.1% DMSO (v/v)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: May 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.95→30.05 Å / Num. obs: 20938 / % possible obs: 95.2 % / Redundancy: 3.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.038 / Rpim(I) all: 0.022 / Rrim(I) all: 0.044 / Net I/σ(I): 16.2 / Num. measured all: 80002
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.95-23.90.218552114280.9670.1280.2534.892.9
8.94-30.053.20.027572330.9990.0130.02332.895.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
Aimless0.7.1data scaling
PDB_EXTRACT3.24data extraction
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdbid 2G43

2g43


Resolution: 1.95→30.07 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.918 / SU B: 3.155 / SU ML: 0.091 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.157 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: Users of this crystal structure: verify our intepretion of the electron density. Additional ambiguous density is observed in the binding pocket of chain B, and is suspected to be low ...Details: Users of this crystal structure: verify our intepretion of the electron density. Additional ambiguous density is observed in the binding pocket of chain B, and is suspected to be low occupancy 3-(5-Phenyl-1,3,4-oxadiazol-2-yl)propanoate. LC-MS evaluation of the ligand shows a
RfactorNum. reflection% reflectionSelection details
Rfree0.2419 1010 4.8 %RANDOM
Rwork0.194 ---
obs0.1962 19928 95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 63.62 Å2 / Biso mean: 25.318 Å2 / Biso min: 12.74 Å2
Baniso -1Baniso -2Baniso -3
1--0.91 Å20 Å2-0.06 Å2
2--1.27 Å20 Å2
3----0.31 Å2
Refinement stepCycle: final / Resolution: 1.95→30.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1731 0 28 170 1929
Biso mean--33.31 33.65 -
Num. residues----227
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0141820
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171545
X-RAY DIFFRACTIONr_angle_refined_deg1.4951.6472472
X-RAY DIFFRACTIONr_angle_other_deg0.9841.6643616
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1735229
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.67323.14689
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.13415276
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.455159
X-RAY DIFFRACTIONr_chiral_restr0.0750.2225
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022144
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02340
LS refinement shellResolution: 1.95→2 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.234 66 -
Rwork0.219 1417 -
all-1483 -
obs--92.46 %

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