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- PDB-1uch: DEUBIQUITINATING ENZYME UCH-L3 (HUMAN) AT 1.8 ANGSTROM RESOLUTION -

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Basic information

Entry
Database: PDB / ID: 1uch
TitleDEUBIQUITINATING ENZYME UCH-L3 (HUMAN) AT 1.8 ANGSTROM RESOLUTION
ComponentsUBIQUITIN C-TERMINAL HYDROLASE UCH-L3
KeywordsCYSTEINE PROTEASE / DEUBIQUITINATING ENZYME / UBIQUITIN / C-TERMINAL HYDROLASE / UBIQUITIN CONJUGATION
Function / homology
Function and homology information


deNEDDylase activity / protein deubiquitination / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / post-translational protein modification / ubiquitin binding / protein catabolic process / UCH proteinases / Neddylation / peptidase activity / ubiquitin-dependent protein catabolic process ...deNEDDylase activity / protein deubiquitination / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / post-translational protein modification / ubiquitin binding / protein catabolic process / UCH proteinases / Neddylation / peptidase activity / ubiquitin-dependent protein catabolic process / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / protein ubiquitination / 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 L3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsJohnston, S.C. / Larsen, C.N. / Cook, W.J. / Wilkinson, K.D. / Hill, C.P.
CitationJournal: EMBO J. / Year: 1997
Title: Crystal structure of a deubiquitinating enzyme (human UCH-L3) at 1.8 A resolution.
Authors: Johnston, S.C. / Larsen, C.N. / Cook, W.J. / Wilkinson, K.D. / Hill, C.P.
History
DepositionOct 6, 1997Processing site: BNL
Revision 1.0Jan 28, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UBIQUITIN C-TERMINAL HYDROLASE UCH-L3


Theoretical massNumber of molelcules
Total (without water)26,2141
Polymers26,2141
Non-polymers00
Water1,874104
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.600, 60.900, 81.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein UBIQUITIN C-TERMINAL HYDROLASE UCH-L3 / UCH-L3 / DUB


Mass: 26213.576 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: HEMATOPOETIC / Cell line: B834 (DE3) / Cellular location: CYTOPLASM / Plasmid: PRSL3 / Cell line (production host): B834 (DE3) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): GAL-MET- AUXOTROPH / References: UniProt: P15374, EC: 3.1.2.15
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 2.37 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.7
Details: PROTEIN AT 12 MG/ML WAS CRYSTALLIZED FROM 26%(W/W) PEG 4000, 200 MM SODIUM ACETATE, 100 MM PIPES PH 6.7 AND 10 MM DTT IN SITTING WELLS AT 4 DEGREES CELSIUS., vapor diffusion - sitting drop, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
112 mg/mlprotein1drop
250 mMTris-HCl1drop
315 mMbeta-mercaptoethanol1drop
41 mMEDTA1drop
526 %(w/v)PEG40001reservoir
6200 mMsodium acetate1reservoir
7100 mMPIPES1reservoir
810 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 1, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 23334 / % possible obs: 98 % / Observed criterion σ(I): -2 / Redundancy: 4.5 % / Biso Wilson estimate: 20.7 Å2 / Rmerge(I) obs: 0.04 / Rsym value: 0.04 / Net I/σ(I): 20
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 3 % / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 5 / Rsym value: 0.19 / % possible all: 93
Reflection shell
*PLUS
% possible obs: 93 %

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Processing

Software
NameVersionClassification
X-PLOR3.843model building
X-PLOR3.843refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.843phasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→6 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: THERE IS A DISORDERED REGION BETWEEN RESIDUES 146 AND 167.
RfactorNum. reflection% reflectionSelection details
Rfree0.294 1056 4.8 %RANDOM
Rwork0.232 ---
obs0.232 21819 97.7 %-
Displacement parametersBiso mean: 28.4 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 1.8→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1661 0 0 312 1973
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.1
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.98
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.170.75
X-RAY DIFFRACTIONx_mcangle_it3.291
X-RAY DIFFRACTIONx_scbond_it3.731
X-RAY DIFFRACTIONx_scangle_it5.671.25
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.373 164 4.7 %
Rwork0.358 3296 -
obs--94.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.98
LS refinement shell
*PLUS
Rfactor obs: 0.358

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