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

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Basic information

Entry
Database: PDB / ID: 6dxh
TitleStructure of USP5 zinc-finger ubiquitin binding domain co-crystallized with 4-(4-tert-butylphenyl)-4-oxobutanoate
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 / Ub-specific processing proteases / protein ubiquitination ...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 / Ub-specific processing proteases / protein ubiquitination / 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
4-(4-tert-butylphenyl)-4-oxobutanoic acid / Ubiquitin carboxyl-terminal hydrolase 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHarding, R.J. / Mann, M.K. / Ravichandran, M. / Ferreira de Freitas, R. / Franzoni, I. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / 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 28, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 18, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,83510
Polymers13,5351
Non-polymers3009
Water97354
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.690, 81.500, 99.660
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-302-

UNX

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Components

#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.: 1 / 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
#2: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 7 / Source method: obtained synthetically
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-HH4 / 4-(4-tert-butylphenyl)-4-oxobutanoic acid


Mass: 234.291 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H18O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 3.58 Å3/Da / Density % sol: 65.62 % / 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), 2.25% 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: 2→31.54 Å / Num. obs: 13422 / % possible obs: 99.4 % / Redundancy: 7 % / CC1/2: 1 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.022 / Rrim(I) all: 0.059 / Net I/σ(I): 23 / Num. measured all: 93762
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
2-2.0570.45166639570.9630.1830.4874.498.3
8.95-31.545.50.0249981800.9990.0110.02660.497.5

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Processing

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

2g43


Resolution: 2→31.56 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.931 / SU B: 4.611 / SU ML: 0.121 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.145 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: Users of this crystal structure: verify our intepretion of the electron density.
RfactorNum. reflection% reflectionSelection details
Rfree0.2512 679 5.1 %RANDOM
Rwork0.2138 ---
obs0.2156 12742 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 77.43 Å2 / Biso mean: 34.154 Å2 / Biso min: 12.71 Å2
Baniso -1Baniso -2Baniso -3
1--3.65 Å20 Å20 Å2
2--6.28 Å20 Å2
3----2.63 Å2
Refinement stepCycle: final / Resolution: 2→31.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms894 0 25 54 973
Biso mean--34.58 41.2 -
Num. residues----117
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.014944
X-RAY DIFFRACTIONr_bond_other_d0.0010.017807
X-RAY DIFFRACTIONr_angle_refined_deg1.561.6491283
X-RAY DIFFRACTIONr_angle_other_deg0.9771.6751886
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6235118
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.85622.39146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.85815146
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.938155
X-RAY DIFFRACTIONr_chiral_restr0.0760.2118
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021118
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02178
LS refinement shellResolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 49 -
Rwork0.308 905 -
all-954 -
obs--98.35 %

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