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- PDB-3ppa: Structure of the Dusp-Ubl domains of Usp15 -

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Basic information

Entry
Database: PDB / ID: 3ppa
TitleStructure of the Dusp-Ubl domains of Usp15
ComponentsUbiquitin carboxyl-terminal hydrolase 15
KeywordsHYDROLASE / Uch / Usp / Dub / deubiquitylation / deubiquitinating enzyme / ubiquitin / ubiquitin specific protease / ubiquitin carboxyterminal hydrolase / cleavage / Usp15 / Dub15 / Ubp15 / endopeptidase / thiolesterase / dusp / domain-swapping / Structural Genomics Consortium (SGC) / phosphoprotein / protease / thiol protease / Ubl conjugation pathway
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 / deubiquitinase activity / transforming growth factor beta receptor binding / K48-linked deubiquitinase activity / transcription elongation-coupled chromatin remodeling ...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 / deubiquitinase activity / transforming growth factor beta receptor binding / K48-linked deubiquitinase activity / transcription elongation-coupled chromatin remodeling / protein deubiquitination / SMAD binding / BMP signaling pathway / Downregulation of TGF-beta receptor signaling / transforming growth factor beta receptor signaling pathway / 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
CITRIC ACID / Ubiquitin carboxyl-terminal hydrolase 15
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsWalker, J.R. / Asinas, A.E. / Dong, A. / Weigelt, J. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / Dhe-Paganon, S. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Structure of the Dusp-Ubl Domains of the Ubiquitin-Specific Protease 15
Authors: Walker, J.R. / Asinas, A.E. / Dong, A. / Weigelt, J. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / Dhe-Paganon, S.
History
DepositionNov 24, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_special_symmetry / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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)27,8965
Polymers27,4161
Non-polymers4804
Water32418
1
A: Ubiquitin carboxyl-terminal hydrolase 15
hetero molecules

A: Ubiquitin carboxyl-terminal hydrolase 15
hetero molecules

A: Ubiquitin carboxyl-terminal hydrolase 15
hetero molecules

A: Ubiquitin carboxyl-terminal hydrolase 15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,58520
Polymers109,6644
Non-polymers1,92116
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565-x,-y+1,z1
crystal symmetry operation9_555-x,-x+y,-z+1/31
crystal symmetry operation12_565x,x-y+1,-z+1/31
Buried area11550 Å2
ΔGint-231 kcal/mol
Surface area44570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.170, 74.170, 194.520
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-322-

CIT

21A-322-

CIT

31A-311-

HOH

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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


Mass: 27415.883 Da / Num. of mol.: 1 / Fragment: Dusp and Ubl domains (UNP residues 6-223)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIAA0529, USP15 / Plasmid: PET28A-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-V2R / References: UniProt: Q9Y4E8, ubiquitinyl hydrolase 1
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 2.82 Å3/Da / Density % sol: 56.33 %
Crystal growTemperature: 291.1 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.5 M ammonium formate, 1.0 M lithium sulfate, 0.1 M citrate pH 5.6; 1 uM dispase added, VAPOR DIFFUSION, SITTING DROP, temperature 291.1K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97921 / Wavelength: 0.97921 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 11, 2010
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 2.35→30 Å / Num. obs: 13829 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 12.7 % / Biso Wilson estimate: 70.85 Å2 / Rsym value: 0.087 / Net I/σ(I): 31.328
Reflection shellResolution: 2.35→2.39 Å / Redundancy: 8.8 % / Mean I/σ(I) obs: 2.21 / Rsym value: 0.808 / % possible all: 97.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
BUSTER2.8.0refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3JYU
Resolution: 2.35→26.8 Å / Cor.coef. Fo:Fc: 0.8959 / Cor.coef. Fo:Fc free: 0.8973 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2852 660 4.83 %RANDOM
Rwork0.2618 ---
obs0.2629 13676 --
Displacement parametersBiso mean: 94.89 Å2
Baniso -1Baniso -2Baniso -3
1--16.8976 Å20 Å20 Å2
2---16.8976 Å20 Å2
3---33.7953 Å2
Refine analyzeLuzzati coordinate error obs: 0.889 Å
Refinement stepCycle: LAST / Resolution: 2.35→26.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1622 0 28 18 1668
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.0116832
X-RAY DIFFRACTIONt_angle_deg1.1322942
X-RAY DIFFRACTIONt_dihedral_angle_d5602
X-RAY DIFFRACTIONt_trig_c_planes402
X-RAY DIFFRACTIONt_gen_planes2395
X-RAY DIFFRACTIONt_it168320
X-RAY DIFFRACTIONt_omega_torsion2.84
X-RAY DIFFRACTIONt_other_torsion19.99
X-RAY DIFFRACTIONt_chiral_improper_torsion2235
X-RAY DIFFRACTIONt_ideal_dist_contact17684
LS refinement shellResolution: 2.35→2.54 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.3029 145 5.34 %
Rwork0.2924 2569 -
all0.2929 2714 -
Refinement TLS params.Method: refined / Origin x: -15.8343 Å / Origin y: 31.2989 Å / Origin z: 31.4737 Å
111213212223313233
T-0.2072 Å2-0.1476 Å20.0071 Å2--0.0958 Å20.0513 Å2---0.3054 Å2
L1.2296 °20.5625 °20.3985 °2-2.1939 °22.7617 °2--6.4225 °2
S-0.1776 Å °0.1554 Å °-0.0204 Å °-0.1182 Å °-0.1869 Å °0.1378 Å °-0.1264 Å °0.0357 Å °0.3646 Å °
Refinement TLS groupSelection details: { A|* }

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