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- PDB-3irt: Crystal Structure of the I93M Mutant of Ubiquitin Carboxy-termina... -

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Basic information

Entry
Database: PDB / ID: 3irt
TitleCrystal Structure of the I93M Mutant of Ubiquitin Carboxy-terminal Hydrolase L1
ComponentsUbiquitin carboxyl-terminal hydrolase isozyme L1
KeywordsHYDROLASE / LIGASE / Ubiquitin Hydrolase / Parkinson's Disease Mutant / Cytoplasm / Disease mutation / Glycoprotein / Oxidation / Polymorphism / Protease / Thiol protease / Ubl conjugation pathway
Function / homology
Function and homology information


axon target recognition / male germ cell proliferation / alpha-2A adrenergic receptor binding / muscle cell development / neuron projection terminus / adult walking behavior / neuromuscular process / eating behavior / axonal transport of mitochondrion / protein deubiquitination ...axon target recognition / male germ cell proliferation / alpha-2A adrenergic receptor binding / muscle cell development / neuron projection terminus / adult walking behavior / neuromuscular process / eating behavior / axonal transport of mitochondrion / protein deubiquitination / regulation of macroautophagy / axon cytoplasm / positive regulation of glycolytic process / negative regulation of MAP kinase activity / ubiquitin binding / response to ischemia / UCH proteinases / cellular response to xenobiotic stimulus / omega peptidase activity / proteasome-mediated ubiquitin-dependent protein catabolic process / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / cysteine-type endopeptidase activity / neuronal cell body / ubiquitin protein ligase binding / endoplasmic reticulum membrane / nucleoplasm / cytoplasm / cytosol
Similarity search - Function
Ubiquitin carboxyl-terminal hydrolase family 1 cysteine active-site. / Ubiquitin C-terminal Hydrolase UCH-l3 / Peptidase C12, ubiquitin carboxyl-terminal hydrolase / Peptidase C12, ubiquitin carboxyl-terminal hydrolase superfamily / Ubiquitin carboxyl-terminal hydrolase, family 1 / Peptidase C12, ubiquitin carboxyl-terminal hydrolase / Papain-like cysteine peptidase superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Ubiquitin carboxyl-terminal hydrolase isozyme L1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.799 Å
AuthorsDavies, C.W. / Maiti, T.K. / Das, C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Ubiquitin vinyl methyl ester binding orients the misaligned active site of the ubiquitin hydrolase UCHL1 into productive conformation.
Authors: Boudreaux, D.A. / Maiti, T.K. / Davies, C.W. / Das, C.
History
DepositionAug 24, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ubiquitin carboxyl-terminal hydrolase isozyme L1
B: Ubiquitin carboxyl-terminal hydrolase isozyme L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6414
Polymers50,5702
Non-polymers712
Water63135
1
A: Ubiquitin carboxyl-terminal hydrolase isozyme L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3202
Polymers25,2851
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ubiquitin carboxyl-terminal hydrolase isozyme L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3202
Polymers25,2851
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)109.938, 109.938, 79.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11A-225-

HOH

21B-225-

HOH

31B-228-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 1:71 or resseq 74:223 )
211chain B and (resseq 1:71 or resseq 74:223 )

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Components

#1: Protein Ubiquitin carboxyl-terminal hydrolase isozyme L1 / UCH-L1 / Ubiquitin thioesterase L1 / Neuron cytoplasmic protein 9.5 / PGP 9.5 / PGP9.5


Mass: 25284.836 Da / Num. of mol.: 2 / Mutation: I93M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PGP9.5, UCHL1 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta
References: UniProt: P09936, ubiquitinyl hydrolase 1, Ligases
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 2.36 Å3/Da / Density % sol: 47.91 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2.4 M Ammonium Sulfate, 0.1 M TRIS Hydrochloride, 0.1 M Sodium Sodium Malonate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0331 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 6, 2009 / Details: mirrors
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0331 Å / Relative weight: 1
ReflectionResolution: 2.8→41.75 Å / Num. all: 11988 / Num. obs: 11988 / % possible obs: 96.1 % / Observed criterion σ(F): 1.78 / Observed criterion σ(I): 1.78 / Redundancy: 12.8 % / Rmerge(I) obs: 0.111 / Rsym value: 0.111 / Net I/σ(I): 19.98
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 1.78 / Rsym value: 0.54 / % possible all: 70

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: One subunit of the asymmetric unit of 2ETL

2etl


Resolution: 2.799→41.748 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 1.09 / Isotropic thermal model: Isotropic / σ(F): 1.34 / Phase error: 27.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2538 582 4.87 %
Rwork0.2106 --
obs0.2126 11957 95.95 %
all-11988 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 63.015 Å2 / ksol: 0.358 e/Å3
Displacement parametersBiso mean: 67.7 Å2
Baniso -1Baniso -2Baniso -3
1-9.9433 Å20 Å2-0 Å2
2--9.9433 Å20 Å2
3----20.2116 Å2
Refinement stepCycle: LAST / Resolution: 2.799→41.748 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3482 0 2 35 3519
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033544
X-RAY DIFFRACTIONf_angle_d0.6414772
X-RAY DIFFRACTIONf_dihedral_angle_d14.3251336
X-RAY DIFFRACTIONf_chiral_restr0.042520
X-RAY DIFFRACTIONf_plane_restr0.002638
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1728X-RAY DIFFRACTIONPOSITIONAL
12B1728X-RAY DIFFRACTIONPOSITIONAL0.035
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7993-3.08090.36341310.30582473X-RAY DIFFRACTION85
3.0809-3.52650.33291530.24552865X-RAY DIFFRACTION99
3.5265-4.44230.22111470.19122936X-RAY DIFFRACTION100
4.4423-41.75260.21891510.18683101X-RAY DIFFRACTION100

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