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- PDB-1th0: Structure of human Senp2 -

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Basic information

Entry
Database: PDB / ID: 1th0
TitleStructure of human Senp2
ComponentsSentrin-specific protease 2
KeywordsCELL CYCLE / HYDROLASE / SUMO / AXAM / SENP / ULP / PROTEASE
Function / homology
Function and homology information


SUMO-specific endopeptidase activity / SUMO is proteolytically processed / deSUMOylase activity / protein desumoylation / regulation of Wnt signaling pathway / fat cell differentiation / protein sumoylation / mRNA transport / nuclear pore / negative regulation of protein ubiquitination ...SUMO-specific endopeptidase activity / SUMO is proteolytically processed / deSUMOylase activity / protein desumoylation / regulation of Wnt signaling pathway / fat cell differentiation / protein sumoylation / mRNA transport / nuclear pore / negative regulation of protein ubiquitination / positive regulation of protein ubiquitination / protein destabilization / Wnt signaling pathway / protein transport / nuclear membrane / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / proteolysis / nucleoplasm / nucleus / cytosol
Similarity search - Function
Adenoviral Proteinase; Chain / Adenoviral Proteinase; Chain A / Ubiquitin-like protease family profile. / Ulp1 protease family, C-terminal catalytic domain / Ulp1 protease family, C-terminal catalytic domain / Papain-like cysteine peptidase superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Sentrin-specific protease 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsReverter, D. / Lima, C.D.
CitationJournal: Structure / Year: 2004
Title: A basis for SUMO protease specificity provided by analysis of human Senp2 and a Senp2-SUMO complex
Authors: Reverter, D. / Lima, C.D.
History
DepositionMay 31, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sentrin-specific protease 2
B: Sentrin-specific protease 2


Theoretical massNumber of molelcules
Total (without water)53,5742
Polymers53,5742
Non-polymers00
Water3,765209
1
A: Sentrin-specific protease 2


Theoretical massNumber of molelcules
Total (without water)26,7871
Polymers26,7871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sentrin-specific protease 2


Theoretical massNumber of molelcules
Total (without water)26,7871
Polymers26,7871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)123.237, 59.228, 94.015
Angle α, β, γ (deg.)90.00, 111.29, 90.00
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121

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Components

#1: Protein Sentrin-specific protease 2 / E.C.3.4.22.- / Sentrin/SUMO-specific protease SENP2 / SMT3-specific isopeptidase 2 / Smt3ip2 / Axam2


Mass: 26787.084 Da / Num. of mol.: 2 / Fragment: catalytic domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SENP2, KIAA1331 / Plasmid: T7 BASED / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 CP RIL
References: UniProt: Q9HC62, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / 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: 2.89 Å3/Da / Density % sol: 57.1 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.25
Details: 20% PEG 4000, 0.2M AMMONIUM SULFATE, 3% XYLITOL, 50MM SODIUM CITRATE, PH6.25, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 1, 2004
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.2→19.46 Å / Num. all: 36438 / Num. obs: 36110 / % possible obs: 99.1 % / Observed criterion σ(I): -1 / Biso Wilson estimate: 22.9 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 20.1
Reflection shellResolution: 2.2→2.25 Å / Rmerge(I) obs: 0.291 / Mean I/σ(I) obs: 2.6 / % possible all: 99.5

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1EUV

1euv


Resolution: 2.2→19.46 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1549986.95 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.247 1372 4.9 %RANDOM
Rwork0.21 ---
obs0.211 27855 86.4 %-
all-32301 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.4953 Å2 / ksol: 0.364336 e/Å3
Displacement parametersBiso mean: 34.9 Å2
Baniso -1Baniso -2Baniso -3
1--1.86 Å20 Å2-3.9 Å2
2---0.11 Å20 Å2
3---1.97 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.36 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2.2→19.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3744 0 0 209 3953
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_improper_angle_d0.75
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.327 200 4.9 %
Rwork0.287 3879 -
obs--76.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP

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