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- PDB-2wp7: Crystal structure of deSUMOylase(DUF862) -

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Basic information

Entry
Database: PDB / ID: 2wp7
TitleCrystal structure of deSUMOylase(DUF862)
ComponentsPPPDE PEPTIDASE DOMAIN-CONTAINING PROTEIN 2
KeywordsHYDROLASE / PHOSPHOPROTEIN / UBIQUITIN-LIKE PROTEIN
Function / homology
Function and homology information


deSUMOylase activity => GO:0016929 / protein modification by small protein removal / regulation of proteasomal ubiquitin-dependent protein catabolic process / protein desumoylation / importin-alpha family protein binding / Hydrolases; Acting on peptide bonds (peptidases) / protein export from nucleus / protein-containing complex / identical protein binding / nucleus / cytosol
Similarity search - Function
PPPDE domains / PPPDE peptidase domain superfamily / PPPDE putative peptidase domain / PPPDE putative peptidase domain / PPPDE peptidase domain / PPPDE domain profile. / endopeptidase fold (from Nostoc punctiforme) / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Desumoylating isopeptidase 1
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsKim, J.H. / Woo, J.S. / Oh, B.H.
CitationJournal: Proteins / Year: 2012
Title: Crystal Structure of Desi-1, a Novel Desumoylase Belonging to a Putative Isopeptidase Superfamily.
Authors: Suh, H.Y. / Kim, J.H. / Woo, J.S. / Ku, B. / Shin, E.J. / Yun, Y. / Oh, B.H.
History
DepositionAug 3, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 1, 2010Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2012Group: Atomic model / Database references / Version format compliance
Revision 1.2Jul 18, 2012Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_sheet
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_sheet.number_strands
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PPPDE PEPTIDASE DOMAIN-CONTAINING PROTEIN 2


Theoretical massNumber of molelcules
Total (without water)18,3991
Polymers18,3991
Non-polymers00
Water95553
1
A: PPPDE PEPTIDASE DOMAIN-CONTAINING PROTEIN 2

A: PPPDE PEPTIDASE DOMAIN-CONTAINING PROTEIN 2


Theoretical massNumber of molelcules
Total (without water)36,7972
Polymers36,7972
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area1990 Å2
ΔGint-22.6 kcal/mol
Surface area14440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.033, 42.033, 164.514
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein PPPDE PEPTIDASE DOMAIN-CONTAINING PROTEIN 2 / PROTEIN FAM152B / DESUMOLYASE


Mass: 18398.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PGEX4T-3 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9CQT7, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 1.92 Å3/Da / Density % sol: 36.11 % / Description: NONE
Crystal growpH: 5.6
Details: 20% (W/V) POLYETHYLENEGLYCOL 3350 AND 200 MM POTASSIUM PHOSPHATE (PH 5.6)

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1
DetectorDetector: CCD / Date: Oct 24, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 11515 / % possible obs: 92.2 % / Observed criterion σ(I): 1 / Redundancy: 7.9 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 33.01
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 3.4 / % possible all: 80

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Processing

Software
NameVersionClassification
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3EBQ

3ebq


Resolution: 1.9→20 Å / Cross valid method: THROUGHOUT / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.2282 596 4.8 %RANDOM
Rwork0.2234 ---
obs0.2234 11499 92.5 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.639 Å20 Å20 Å2
2--1.639 Å20 Å2
3----3.277 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1225 0 0 53 1278
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005778
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.33148
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it

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