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- PDB-5k16: Crystal structure of free Ubiquitin-specific protease 12 -

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Basic information

Entry
Database: PDB / ID: 5k16
TitleCrystal structure of free Ubiquitin-specific protease 12
ComponentsUbiquitin carboxyl-terminal hydrolase 12
KeywordsHYDROLASE / deubiquitination / deubiquitnating enzyme / DUB
Function / homology
Function and homology information


protein deubiquitination / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Ub-specific processing proteases / cysteine-type endopeptidase activity / proteolysis / nucleoplasm / metal ion binding / nucleus / plasma membrane ...protein deubiquitination / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Ub-specific processing proteases / cysteine-type endopeptidase activity / proteolysis / nucleoplasm / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
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. / Cysteine proteinases / Cathepsin B; Chain A / Papain-like cysteine peptidase superfamily ...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. / Cysteine proteinases / Cathepsin B; Chain A / Papain-like cysteine peptidase superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Ubiquitin carboxyl-terminal hydrolase 12
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.599 Å
AuthorsLi, H. / D'Andrea, A.D. / Zheng, N.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Mol.Cell / Year: 2016
Title: Allosteric Activation of Ubiquitin-Specific Proteases by beta-Propeller Proteins UAF1 and WDR20.
Authors: Li, H. / Lim, K.S. / Kim, H. / Hinds, T.R. / Jo, U. / Mao, H. / Weller, C.E. / Sun, J. / Chatterjee, C. / D'Andrea, A.D. / Zheng, N.
History
DepositionMay 17, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2016Group: Database references
Revision 1.2Nov 1, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_struct_assembly_auth_evidence / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 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 12
B: Ubiquitin carboxyl-terminal hydrolase 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,8286
Polymers82,5132
Non-polymers3154
Water1,00956
1
A: Ubiquitin carboxyl-terminal hydrolase 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4143
Polymers41,2571
Non-polymers1582
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ubiquitin carboxyl-terminal hydrolase 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4143
Polymers41,2571
Non-polymers1582
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2790 Å2
ΔGint-10 kcal/mol
Surface area30250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.396, 109.636, 134.193
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsMonomer as determined by size-exclusion chromatography

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Components

#1: Protein Ubiquitin carboxyl-terminal hydrolase 12 / Deubiquitinating enzyme 12 / Ubiquitin thioesterase 12 / Ubiquitin-hydrolyzing enzyme 1 / Ubiquitin- ...Deubiquitinating enzyme 12 / Ubiquitin thioesterase 12 / Ubiquitin-hydrolyzing enzyme 1 / Ubiquitin-specific-processing protease 12


Mass: 41256.684 Da / Num. of mol.: 2 / Fragment: residues 16-370
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: USP12, UBH1, USP12L1 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: O75317, ubiquitinyl hydrolase 1
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 2.52 Å3/Da / Density % sol: 51.24 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M Tris-HCl, 18% PEG 3350, 0.2 M Lithium Sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.599→50 Å / Num. obs: 24515 / % possible obs: 99.9 % / Redundancy: 4 % / Rmerge(I) obs: 0.091 / Rsym value: 0.105 / Net I/σ(I): 14.3
Reflection shellResolution: 2.599→2.64 Å / Redundancy: 4 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 1.4 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIXdev_1760refinement
PHENIXphasing
Cootmodel building
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3M99

3m99


Resolution: 2.599→42.451 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2459 1256 5.12 %
Rwork0.1899 --
obs0.1927 24515 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.599→42.451 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5129 0 14 56 5199
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015255
X-RAY DIFFRACTIONf_angle_d1.2327118
X-RAY DIFFRACTIONf_dihedral_angle_d15.1851859
X-RAY DIFFRACTIONf_chiral_restr0.046801
X-RAY DIFFRACTIONf_plane_restr0.005914
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.599-2.7030.34141500.27592506X-RAY DIFFRACTION99
2.703-2.8260.35231510.25232534X-RAY DIFFRACTION100
2.826-2.9750.28631310.24132537X-RAY DIFFRACTION100
2.975-3.16130.27941530.21762532X-RAY DIFFRACTION100
3.1613-3.40530.29551580.21082545X-RAY DIFFRACTION100
3.4053-3.74780.25651140.1922624X-RAY DIFFRACTION100
3.7478-4.28970.22261460.17122568X-RAY DIFFRACTION100
4.2897-5.40280.17851240.15322640X-RAY DIFFRACTION100
5.4028-42.4570.21981290.17512773X-RAY DIFFRACTION100

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