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- PDB-4a3p: Structure of USP15 DUSP-UBL deletion mutant -

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Basic information

Entry
Database: PDB / ID: 4a3p
TitleStructure of USP15 DUSP-UBL deletion mutant
ComponentsUBIQUITIN CARBOXYL-TERMINAL HYDROLASE 15
KeywordsHYDROLASE
Function / homology
Function and homology information


regulation of intrinsic apoptotic signaling pathway in response to osmotic stress by p53 class mediator / negative regulation of antifungal innate immune response / protein K27-linked deubiquitination / positive regulation of RIG-I signaling pathway / ubiquitin-modified histone reader activity / monoubiquitinated protein deubiquitination / transforming growth factor beta receptor binding / deubiquitinase activity / K48-linked deubiquitinase activity / protein deubiquitination ...regulation of intrinsic apoptotic signaling pathway in response to osmotic stress by p53 class mediator / negative regulation of antifungal innate immune response / protein K27-linked deubiquitination / positive regulation of RIG-I signaling pathway / ubiquitin-modified histone reader activity / monoubiquitinated protein deubiquitination / transforming growth factor beta receptor binding / deubiquitinase activity / K48-linked deubiquitinase activity / protein deubiquitination / transcription elongation-coupled chromatin remodeling / SMAD binding / BMP signaling pathway / transforming growth factor beta receptor signaling pathway / Downregulation of TGF-beta receptor signaling / negative regulation of transforming growth factor beta receptor signaling pathway / UCH proteinases / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / nuclear body / Ub-specific processing proteases / cysteine-type endopeptidase activity / mitochondrion / proteolysis / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
DUSP-like / DUSP-like / Ubiquitin-like domain, USP-type / Ubiquitin-like domain / Peptidase C19, ubiquitin-specific peptidase, DUSP domain / DUSP-like superfamily / DUSP domain / DUSP domain profile. / Domain in ubiquitin-specific proteases. / Ubiquitin carboxyl-terminal hydrolase, C-terminal ...DUSP-like / DUSP-like / Ubiquitin-like domain, USP-type / Ubiquitin-like domain / Peptidase C19, ubiquitin-specific peptidase, DUSP domain / DUSP-like superfamily / DUSP domain / DUSP domain profile. / Domain in ubiquitin-specific proteases. / Ubiquitin carboxyl-terminal hydrolase, C-terminal / Ubiquitin-specific protease C-terminal / : / RNA 3'-terminal phosphate cyclase/enolpyruvate transferase, alpha/beta / Ubiquitin specific protease (USP) domain signature 2. / Ubiquitin specific protease (USP) domain signature 1. / Ubiquitin specific protease, conserved site / Peptidase C19, ubiquitin carboxyl-terminal hydrolase / Ubiquitin carboxyl-terminal hydrolase / Ubiquitin specific protease domain / Ubiquitin specific protease (USP) domain profile. / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Papain-like cysteine peptidase superfamily / Ubiquitin-like (UB roll) / Ubiquitin-like domain superfamily / Roll / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / IODIDE ION / Ubiquitin carboxyl-terminal hydrolase 15
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsElliott, P.R. / Liu, H. / Pastok, M.W. / Grossmann, G.J. / Rigden, D.J. / Clague, M.J. / Urbe, S. / Barsukov, I.L.
CitationJournal: FEBS Lett. / Year: 2011
Title: Structural Variability of the Ubiquitin Specific Protease Dusp-Ubl Double Domains.
Authors: Elliott, P.R. / Liu, H. / Pastok, M.W. / Grossmann, G.J. / Rigden, D.J. / Clague, M.J. / Urbe, S. / Barsukov, I.L.
History
DepositionOct 3, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 16, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3303
Polymers25,1441
Non-polymers1862
Water4,017223
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.950, 44.250, 56.150
Angle α, β, γ (deg.)90.00, 104.33, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 15 / DEUBIQUITINATING ENZYME 15 / UBIQUITIN THIOLESTERASE 15 / UBIQUITIN-SPECIFIC-PROCESSING PROTEASE 15 ...DEUBIQUITINATING ENZYME 15 / UBIQUITIN THIOLESTERASE 15 / UBIQUITIN-SPECIFIC-PROCESSING PROTEASE 15 / UNPH-2 / UNPH4 / USP15


Mass: 25144.334 Da / Num. of mol.: 1 / Fragment: DUSP-UBL, RESIDUES 6-123,127-223
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q9Y4E8, ubiquitinyl hydrolase 1
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: I
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUES 124-126 (VKH) WERE SUB-CLONED OUT OF THE SEQUENCE TO GENERATE A DELETION MUTANT. F123 IS ...RESIDUES 124-126 (VKH) WERE SUB-CLONED OUT OF THE SEQUENCE TO GENERATE A DELETION MUTANT. F123 IS PEPTIDE LINKED TO C127.

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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: 2.19 Å3/Da / Density % sol: 43.7 % / Description: NONE
Crystal growpH: 7 / Details: 1.9 M (NH4)2SO4, 100 MM HEPES PH 7.0, 200 MM KI.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.98
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Details: DUAL SLITS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.4→34.33 Å / Num. obs: 39193 / % possible obs: 92.8 % / Observed criterion σ(I): 13.4 / Redundancy: 2.2 % / Biso Wilson estimate: 27.2 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 13.4
Reflection shellResolution: 1.4→1.47 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 3.9 / % possible all: 95

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3PV1

3pv1


Resolution: 1.4→27.2 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.932 / SU B: 2.624 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R: 0.071 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22126 1981 5.1 %RANDOM
Rwork0.153 ---
obs0.15652 37168 92.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.149 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å2-0.13 Å2
2--0.04 Å20 Å2
3----0.14 Å2
Refinement stepCycle: LAST / Resolution: 1.4→27.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1713 0 5 223 1941
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.021788
X-RAY DIFFRACTIONr_bond_other_d0.0010.021218
X-RAY DIFFRACTIONr_angle_refined_deg1.8911.9552427
X-RAY DIFFRACTIONr_angle_other_deg1.21232987
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6675219
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.10925.34986
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.37615325
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.948158
X-RAY DIFFRACTIONr_chiral_restr0.1240.2266
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021958
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02354
X-RAY DIFFRACTIONr_nbd_refined0.3210.2625
X-RAY DIFFRACTIONr_nbd_other0.2360.21151
X-RAY DIFFRACTIONr_nbtor_refined0.1910.2851
X-RAY DIFFRACTIONr_nbtor_other0.110.2897
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2640.244
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4410.291
X-RAY DIFFRACTIONr_symmetry_vdw_other0.5050.262
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3240.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it13.5091.9221788
X-RAY DIFFRACTIONr_mcbond_other13.8681.9731218
X-RAY DIFFRACTIONr_mcangle_it15.3082.8412420
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr16.08333006
X-RAY DIFFRACTIONr_sphericity_free28.951564
X-RAY DIFFRACTIONr_sphericity_bonded13.99953128
LS refinement shellResolution: 1.398→1.434 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 143 -
Rwork0.205 2714 -
obs--94.42 %

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