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- PDB-6lvs: USP14 catalytic domain mutant C114S -

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Basic information

Entry
Database: PDB / ID: 6lvs
TitleUSP14 catalytic domain mutant C114S
ComponentsUbiquitin carboxyl-terminal hydrolase 14
KeywordsHYDROLASE / Ubiquitin Dependent Protein Catabolic Process / Protein Deubiquitination
Function / homology
Function and homology information


negative regulation of ERAD pathway / deubiquitinase activity / regulation of chemotaxis / protein K48-linked deubiquitination / endopeptidase inhibitor activity / K63-linked deubiquitinase activity / proteasome binding / negative regulation of ubiquitin-dependent protein catabolic process / presynaptic cytosol / regulation of proteasomal protein catabolic process ...negative regulation of ERAD pathway / deubiquitinase activity / regulation of chemotaxis / protein K48-linked deubiquitination / endopeptidase inhibitor activity / K63-linked deubiquitinase activity / proteasome binding / negative regulation of ubiquitin-dependent protein catabolic process / presynaptic cytosol / regulation of proteasomal protein catabolic process / proteasome complex / Regulation of NF-kappa B signaling / cytoplasmic vesicle / chemical synaptic transmission / proteasome-mediated ubiquitin-dependent protein catabolic process / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Ub-specific processing proteases / innate immune response / cysteine-type endopeptidase activity / nucleolus / glutamatergic synapse / cell surface / endoplasmic reticulum / extracellular exosome / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Ubiquitin carboxyl-terminal hydrolase 14-like / 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 ...Ubiquitin carboxyl-terminal hydrolase 14-like / 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 domain signature. / Ubiquitin conserved site / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / FORMIC ACID / Ubiquitin carboxyl-terminal hydrolase 14
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.73 Å
AuthorsLin, H.C. / Lin, T.H. / Chou, C.Y.
CitationJournal: To Be Published
Title: USP14 catalytic domain mutant C114S
Authors: Lin, H.C.
History
DepositionFeb 4, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 18, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ubiquitin carboxyl-terminal hydrolase 14
B: Ubiquitin carboxyl-terminal hydrolase 14
C: Ubiquitin carboxyl-terminal hydrolase 14
D: Ubiquitin carboxyl-terminal hydrolase 14
E: Ubiquitin carboxyl-terminal hydrolase 14
F: Ubiquitin carboxyl-terminal hydrolase 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)285,90395
Polymers281,8946
Non-polymers4,01089
Water6,377354
1
A: Ubiquitin carboxyl-terminal hydrolase 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,59014
Polymers46,9821
Non-polymers60713
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ubiquitin carboxyl-terminal hydrolase 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,92121
Polymers46,9821
Non-polymers93920
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Ubiquitin carboxyl-terminal hydrolase 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,78319
Polymers46,9821
Non-polymers80118
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Ubiquitin carboxyl-terminal hydrolase 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,37310
Polymers46,9821
Non-polymers3919
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Ubiquitin carboxyl-terminal hydrolase 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,85419
Polymers46,9821
Non-polymers87218
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Ubiquitin carboxyl-terminal hydrolase 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,38212
Polymers46,9821
Non-polymers40011
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.506, 160.422, 90.311
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Ubiquitin carboxyl-terminal hydrolase 14 / Deubiquitinating enzyme 14 / Ubiquitin thioesterase 14 / Ubiquitin-specific-processing protease 14


Mass: 46982.258 Da / Num. of mol.: 6 / Fragment: catalytic domain / Mutation: C114S, deletion of 223-231
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: USP14, TGT / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P54578, ubiquitinyl hydrolase 1

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Non-polymers , 6 types, 443 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical...
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 41 / Source method: obtained synthetically / Formula: Na
#4: Chemical...
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical
ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6OS
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 354 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.08 Å3/Da / Density % sol: 40.87 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop / Details: 0.2M HcooNa, 0.1M BICINE, 20% PEGmme 5000

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.9998 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Nov 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9998 Å / Relative weight: 1
ReflectionResolution: 2.73→50 Å / Num. obs: 62014 / % possible obs: 99.7 % / Redundancy: 3 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 17.4
Reflection shellResolution: 2.73→2.83 Å / Num. unique obs: 6191 / CC1/2: 0.844

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2AYN

2ayn


Resolution: 2.73→28.49 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.87 / SU B: 14.948 / SU ML: 0.3 / Cross valid method: THROUGHOUT / ESU R Free: 0.413 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27677 3065 5 %RANDOM
Rwork0.197 ---
obs0.20093 58008 98.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.577 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å20 Å20.24 Å2
2---0.14 Å2-0 Å2
3----0.1 Å2
Refinement stepCycle: 1 / Resolution: 2.73→28.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15925 0 231 354 16510
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.01316375
X-RAY DIFFRACTIONr_bond_other_d0.0010.01715267
X-RAY DIFFRACTIONr_angle_refined_deg1.2851.64421969
X-RAY DIFFRACTIONr_angle_other_deg1.0761.57835511
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.84651957
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.95223.061846
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.746153009
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4381588
X-RAY DIFFRACTIONr_chiral_restr0.140.22087
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0217898
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023390
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.254.8677903
X-RAY DIFFRACTIONr_mcbond_other2.254.8677904
X-RAY DIFFRACTIONr_mcangle_it3.8467.2799835
X-RAY DIFFRACTIONr_mcangle_other3.8467.2799836
X-RAY DIFFRACTIONr_scbond_it2.1115.1828472
X-RAY DIFFRACTIONr_scbond_other2.1115.1828473
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.6237.61412135
X-RAY DIFFRACTIONr_long_range_B_refined9.77556.5317844
X-RAY DIFFRACTIONr_long_range_B_other9.77556.53417845
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.73→2.878 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.324 372 -
Rwork0.24 7703 -
obs--89.18 %

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