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- PDB-4jkj: Crystal Structure of the S18Y Variant of Ubiquitin Carboxy-termin... -

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Basic information

Entry
Database: PDB / ID: 4jkj
TitleCrystal Structure of the S18Y Variant of Ubiquitin Carboxy-terminal Hydrolase L1
ComponentsUbiquitin carboxyl-terminal hydrolase isozyme L1
KeywordsHYDROLASE / Ubiquitin 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 / 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: 2.151 Å
AuthorsDavies, C.W. / Ringe, D. / Petsko, G.A. / Das, C.
CitationJournal: To be Published
Title: Crystal Structure of the S18Y Variant of Ubiquitin Carboxy-terminal Hydrolase L1
Authors: Davies, C.W. / Ringe, D. / Petsko, G.A. / Das, C.
History
DepositionMar 9, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 28, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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_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

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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)50,9745
Polymers50,6862
Non-polymers2883
Water1,71195
1
A: Ubiquitin carboxyl-terminal hydrolase isozyme L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5353
Polymers25,3431
Non-polymers1922
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)25,4392
Polymers25,3431
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
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)102,14012
Polymers101,3724
Non-polymers7698
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
Buried area9610 Å2
ΔGint-37 kcal/mol
Surface area34930 Å2
MethodPISA
4
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)101,7568
Polymers101,3724
Non-polymers3844
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
Buried area9360 Å2
ΔGint-40 kcal/mol
Surface area34530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.585, 109.585, 79.715
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212

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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: 25342.895 Da / Num. of mol.: 2 / Mutation: S18Y
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) / Strain (production host): Rosetta / References: UniProt: P09936, ubiquitinyl hydrolase 1
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 47.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2.4M Ammonium sulfate, 0.1M HEPES, 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-D / Wavelength: 0.97 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 9, 2006 / Details: mirrors
RadiationMonochromator: Si 111 Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. all: 26943 / Num. obs: 26890 / % possible obs: 99.9 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 4 / Redundancy: 12.5 % / Rsym value: 0.064 / Net I/σ(I): 41.4
Reflection shell
Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique allRsym valueDiffraction-ID% possible all
2.15-2.2311.34.0526170.644199.9
2.23-2.3212.15.4326380.4951100
2.32-2.4212.68.2126640.3621100
2.42-2.5512.813.1626430.2281100
2.55-2.7112.816.6826640.1881100
2.71-2.9212.922.7926730.1291100

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ETL

2etl


Resolution: 2.151→33.208 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2446 1355 5.04 %Random
Rwork0.1971 ---
all0.1995 26943 --
obs0.198 26890 99.85 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.247 Å2 / ksol: 0.394 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.2966 Å2-0 Å2-0 Å2
2--3.2966 Å20 Å2
3----6.5932 Å2
Refinement stepCycle: LAST / Resolution: 2.151→33.208 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3490 0 15 95 3600
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073566
X-RAY DIFFRACTIONf_angle_d1.0754807
X-RAY DIFFRACTIONf_dihedral_angle_d16.0851339
X-RAY DIFFRACTIONf_chiral_restr0.081522
X-RAY DIFFRACTIONf_plane_restr0.004639
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.151-2.22790.32291330.25472481X-RAY DIFFRACTION100
2.2279-2.31710.32971230.23052505X-RAY DIFFRACTION100
2.3171-2.42250.24321310.21532530X-RAY DIFFRACTION100
2.4225-2.55020.24771490.19412487X-RAY DIFFRACTION100
2.5502-2.70990.2551240.20512533X-RAY DIFFRACTION100
2.7099-2.9190.28221560.20632515X-RAY DIFFRACTION100
2.919-3.21250.22981370.19962550X-RAY DIFFRACTION100
3.2125-3.67690.24021360.18392566X-RAY DIFFRACTION100
3.6769-4.63050.20711400.17092612X-RAY DIFFRACTION100
4.6305-33.21180.25281260.20892756X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.5934-0.4586-0.83623.26830.96623.4099-0.0165-0.04090.08720.09620.07050.10060.0591-0.1004-0.03760.1173-0.0205-0.03440.14350.04720.179736.7347-14.444-12.8767
23.6719-0.2578-1.24394.58161.47035.1657-0.16310.2083-0.2430.0687-0.1397-0.13050.5296-0.34550.12290.092-0.07650.02020.0642-0.01380.135347.094-21.9702-51.5482
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resseq 1:223)
2X-RAY DIFFRACTION2(chain B and resseq 1:223)

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