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- PDB-8xi7: The Crystal Structure of UCHL1 from Biortus. -

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Basic information

Entry
Database: PDB / ID: 8xi7
TitleThe Crystal Structure of UCHL1 from Biortus.
ComponentsUbiquitin carboxyl-terminal hydrolase isozyme L1
KeywordsHYDROLASE / 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. / Peptidase C12, ubiquitin carboxyl-terminal hydrolase superfamily / Ubiquitin carboxyl-terminal hydrolase, family 1 / Peptidase C12, ubiquitin carboxyl-terminal hydrolase / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
Ubiquitin carboxyl-terminal hydrolase isozyme L1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsWang, F. / Cheng, W. / Yuan, Z. / Qi, J. / Shen, Z.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: The Crystal Structure of UCHL1 from Biortus.
Authors: Wang, F. / Cheng, W. / Yuan, Z. / Qi, J. / Shen, Z.
History
DepositionDec 19, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 6, 2024Provider: repository / Type: Initial release

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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)49,9655
Polymers49,7112
Non-polymers2543
Water4,161231
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)109.216, 109.216, 79.379
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11B-485-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ALA / End label comp-ID: ALA / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 1 - 222 / Label seq-ID: 1 - 222

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

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


Mass: 24855.344 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UCHL1 / Production host: Escherichia coli (E. coli) / References: UniProt: P09936, ubiquitinyl hydrolase 1
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / Source method: isolated from a natural source / Formula: H2O
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: 2.38 Å3/Da / Density % sol: 48.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 2.1M ammonium sulfate, 2% PEG 400, 100mM HEPES, pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.95374 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 21, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95374 Å / Relative weight: 1
ReflectionResolution: 1.95→48.84 Å / Num. obs: 35583 / % possible obs: 100 % / Redundancy: 19.2 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 20.9
Reflection shellResolution: 1.95→2 Å / Rmerge(I) obs: 1.056 / Num. unique obs: 2445

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→48.84 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.948 / SU B: 3.923 / SU ML: 0.111 / Cross valid method: FREE R-VALUE / ESU R: 0.172 / ESU R Free: 0.153
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2311 1855 5.217 %
Rwork0.1939 33701 -
all0.196 --
obs-35556 99.947 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 40.415 Å2
Baniso -1Baniso -2Baniso -3
1-1.41 Å2-0 Å2-0 Å2
2--1.41 Å2-0 Å2
3----2.819 Å2
Refinement stepCycle: LAST / Resolution: 1.95→48.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3470 0 14 231 3715
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0123559
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163389
X-RAY DIFFRACTIONr_angle_refined_deg1.061.6444795
X-RAY DIFFRACTIONr_angle_other_deg0.3611.5777832
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9145446
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.821518
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.39410645
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.47210176
X-RAY DIFFRACTIONr_chiral_restr0.0540.2524
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024186
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02790
X-RAY DIFFRACTIONr_nbd_refined0.2040.2728
X-RAY DIFFRACTIONr_symmetry_nbd_other0.190.22983
X-RAY DIFFRACTIONr_nbtor_refined0.1730.21718
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0740.21939
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2185
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0490.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1150.233
X-RAY DIFFRACTIONr_nbd_other0.1490.2149
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1680.213
X-RAY DIFFRACTIONr_mcbond_it2.8573.9871778
X-RAY DIFFRACTIONr_mcbond_other2.8563.9881778
X-RAY DIFFRACTIONr_mcangle_it4.3427.1532220
X-RAY DIFFRACTIONr_mcangle_other4.3417.1552221
X-RAY DIFFRACTIONr_scbond_it3.6044.5361781
X-RAY DIFFRACTIONr_scbond_other3.6074.5391774
X-RAY DIFFRACTIONr_scangle_it5.858.072573
X-RAY DIFFRACTIONr_scangle_other5.8558.0752562
X-RAY DIFFRACTIONr_lrange_it8.00639.7713962
X-RAY DIFFRACTIONr_lrange_other8.00939.4933930
X-RAY DIFFRACTIONr_ncsr_local_group_10.0960.056857
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.095510.05009
12AX-RAY DIFFRACTIONLocal ncs0.095510.05009
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.0010.311310.2612426X-RAY DIFFRACTION100
2.001-2.0550.2431420.2342387X-RAY DIFFRACTION100
2.055-2.1150.2731470.2312300X-RAY DIFFRACTION99.9592
2.115-2.180.2461120.2192266X-RAY DIFFRACTION100
2.18-2.2510.251240.2182182X-RAY DIFFRACTION100
2.251-2.330.2451170.2062135X-RAY DIFFRACTION100
2.33-2.4180.2821320.2082034X-RAY DIFFRACTION100
2.418-2.5160.2571150.21969X-RAY DIFFRACTION99.9041
2.516-2.6280.2751190.2071874X-RAY DIFFRACTION100
2.628-2.7560.2491030.2171844X-RAY DIFFRACTION100
2.756-2.9040.26980.2121714X-RAY DIFFRACTION100
2.904-3.080.244820.2071664X-RAY DIFFRACTION100
3.08-3.2910.244790.1971570X-RAY DIFFRACTION99.9394
3.291-3.5540.24550.1881480X-RAY DIFFRACTION100
3.554-3.8910.185740.1761343X-RAY DIFFRACTION100
3.891-4.3470.193630.1611234X-RAY DIFFRACTION100
4.347-5.0120.173560.1521107X-RAY DIFFRACTION100
5.012-6.1230.238400.185957X-RAY DIFFRACTION100
6.123-8.5920.206440.194746X-RAY DIFFRACTION99.6217
8.592-48.840.262220.206469X-RAY DIFFRACTION98.5944

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