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- PDB-2etl: Crystal Structure of Ubiquitin Carboxy-terminal Hydrolase L1 (UCH-L1) -

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Basic information

Entry
Database: PDB / ID: 2etl
TitleCrystal Structure of Ubiquitin Carboxy-terminal Hydrolase L1 (UCH-L1)
ComponentsUbiquitin carboxyl-terminal hydrolase isozyme L1
KeywordsHYDROLASE / LIGASE / Deubiquitinating Thiol Hydrolase
Function / homology
Function and homology information


axon target recognition / male germ cell proliferation / alpha-2A adrenergic receptor binding / muscle cell development / neuron projection terminus / signaling receptor inhibitor activity / adult walking behavior / eating behavior / neuromuscular process / axonal transport of mitochondrion ...axon target recognition / male germ cell proliferation / alpha-2A adrenergic receptor binding / muscle cell development / neuron projection terminus / signaling receptor inhibitor activity / adult walking behavior / eating behavior / neuromuscular process / axonal transport of mitochondrion / protein deubiquitination / regulation of macroautophagy / negative regulation of MAPK cascade / axon cytoplasm / positive regulation of glycolytic process / response to ischemia / ubiquitin binding / protein catabolic process / cellular response to xenobiotic stimulus / UCH proteinases / ribosome binding / 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 / Ubiquitin carboxyl-terminal hydrolase (UCH) catalytic domain profile. / 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: 2.4 Å
AuthorsDas, C. / Hoang, Q.Q. / Kreinbring, C.A. / Luchansky, S.J. / Meray, R.K. / Ray, S.S. / Lansbury, P.T. / Ringe, D. / Petsko, G.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2006
Title: Structural basis for conformational plasticity of the Parkinson's disease-associated ubiquitin hydrolase UCH-L1.
Authors: Das, C. / Hoang, Q.Q. / Kreinbring, C.A. / Luchansky, S.J. / Meray, R.K. / Ray, S.S. / Lansbury, P.T. / Ringe, D. / Petsko, G.A.
History
DepositionOct 27, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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 1.5Apr 3, 2024Group: Refinement description / Category: 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)50,6756
Polymers50,5342
Non-polymers1424
Water1,928107
1
A: Ubiquitin carboxyl-terminal hydrolase isozyme L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3383
Polymers25,2671
Non-polymers712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ubiquitin carboxyl-terminal hydrolase isozyme L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3383
Polymers25,2671
Non-polymers712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Ubiquitin carboxyl-terminal hydrolase isozyme L1
hetero molecules

B: Ubiquitin carboxyl-terminal hydrolase isozyme L1
hetero molecules

B: Ubiquitin carboxyl-terminal hydrolase isozyme L1
hetero molecules

B: Ubiquitin carboxyl-terminal hydrolase isozyme L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,35112
Polymers101,0674
Non-polymers2848
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-x+2,-y+1,z1
crystal symmetry operation3_645-y+3/2,x-1/2,z1
crystal symmetry operation4_565y+1/2,-x+3/2,z1
Buried area11020 Å2
ΔGint-106 kcal/mol
Surface area34070 Å2
MethodPISA, PQS
4
A: Ubiquitin carboxyl-terminal hydrolase isozyme L1
hetero molecules

A: Ubiquitin carboxyl-terminal hydrolase isozyme L1
hetero molecules

A: Ubiquitin carboxyl-terminal hydrolase isozyme L1
hetero molecules

A: Ubiquitin carboxyl-terminal hydrolase isozyme L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,35112
Polymers101,0674
Non-polymers2848
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_545-y+1/2,x-1/2,z1
crystal symmetry operation4_555y+1/2,-x+1/2,z1
MethodPQS
Unit cell
Length a, b, c (Å)110.097, 110.097, 79.489
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
DetailsThe biological assembly is a monomer, a subunit of the assymetric unit which contains two copies of the protein molecule.

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Components

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


Mass: 25266.799 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UCHL1 / Plasmid: pGEX-6P1 / Production host: Escherichia coli (E. coli)
References: UniProt: P09936, ubiquitinyl hydrolase 1, Ligases
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2.38 Å3/Da / Density % sol: 48.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2.4 M Ammonium Sulfate, 0.1 M HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98397 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 29, 2005 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98397 Å / Relative weight: 1
ReflectionResolution: 2.4→41.9 Å / Num. all: 34753 / Num. obs: 34753 / % possible obs: 100 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 14.1 % / Rmerge(I) obs: 0.088 / Χ2: 0.997
Reflection shellResolution: 2.4→2.49 Å / % possible obs: 99.7 % / Redundancy: 14.3 % / Rmerge(I) obs: 0.773 / Num. measured obs: 1925 / Χ2: 1.17 / % possible all: 99.7

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Phasing

Phasing MRRfactor: 0.554 / Cor.coef. Fo:Fc: 0.284
Highest resolutionLowest resolution
Rotation3.5 Å21.99 Å
Translation3.5 Å21.99 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement
PDB_EXTRACT1.7data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Homology model based on UCH-L3

Resolution: 2.4→41.9 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.274 3369 9.2 %RANDOM
Rwork0.223 ---
all0.227 34753 --
obs0.227 34753 95.1 %-
Solvent computationBsol: 47.87 Å2
Displacement parametersBiso mean: 49.283 Å2
Baniso -1Baniso -2Baniso -3
1--4.038 Å20 Å20 Å2
2---4.038 Å20 Å2
3---8.076 Å2
Refinement stepCycle: LAST / Resolution: 2.4→41.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3482 0 4 107 3593
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramCNS_TOPPAR:protein.top
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.paramCNS_TOPPAR:dna-rna.top
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top
X-RAY DIFFRACTION4CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top

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