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- PDB-3oqc: Ubiquitin-fold modifier 1 Specific Protease, UfSP2 -

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Basic information

Entry
Database: PDB / ID: 3oqc
TitleUbiquitin-fold modifier 1 Specific Protease, UfSP2
ComponentsUfm1-specific protease 2
KeywordsHYDROLASE / DPH motif Cys protease
Function / homology
Function and homology information


deUFMylase activity / negative regulation of proteolysis involved in protein catabolic process / regulation of type II interferon production / regulation of intracellular estrogen receptor signaling pathway / ribosome disassembly / rescue of stalled ribosome / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / endoplasmic reticulum / proteolysis / nucleus / cytoplasm
Similarity search - Function
: / Ubiquitin-fold modifier 1 specific protease 2, N-terminal / Cathepsin B; Chain A - #130 / Peptidase C78, ubiquitin fold modifier-specific peptidase 1/ 2 / Peptidase family C78 / Cathepsin B; Chain A / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Ufm1-specific protease 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 Å
AuthorsHa, B.H. / Chung, C.H. / Kim, E.E.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Structure of ubiquitin-fold modifier 1-specific protease UfSP2
Authors: Ha, B.H. / Jeon, Y.J. / Shin, S.C. / Tatsumi, K. / Komatsu, M. / Tanaka, K. / Watson, C.M. / Wallis, G. / Chung, C.H. / Kim, E.E.
History
DepositionSep 2, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 12, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 26, 2014Group: Database references
Revision 1.3Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ufm1-specific protease 2
B: Ufm1-specific protease 2


Theoretical massNumber of molelcules
Total (without water)109,3482
Polymers109,3482
Non-polymers00
Water1,928107
1
A: Ufm1-specific protease 2


Theoretical massNumber of molelcules
Total (without water)54,6741
Polymers54,6741
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ufm1-specific protease 2


Theoretical massNumber of molelcules
Total (without water)54,6741
Polymers54,6741
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)184.533, 56.041, 143.269
Angle α, β, γ (deg.)90.00, 128.01, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Ufm1-specific protease 2 / UfSP2


Mass: 54674.191 Da / Num. of mol.: 2 / Mutation: K94R, R128A, C294S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET28a / Production host: Escherichia coli (E. coli)
References: UniProt: Q99K23, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2.67 Å3/Da / Density % sol: 53.91 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 40mM K2HPO4, 12% PEG 3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 0.97947, 0.979613, 0.97177, 1.0
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 7, 2008
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979471
20.9796131
30.971771
411
ReflectionResolution: 2.6→46.1 Å / Num. obs: 35942 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.6→2.69 Å / % possible all: 96.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
REFMAC5.5.0072refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.6→46.1 Å / Cor.coef. Fo:Fc: 0.896 / Cor.coef. Fo:Fc free: 0.841 / SU B: 13.538 / SU ML: 0.293 / Cross valid method: THROUGHOUT / ESU R Free: 0.354 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29807 1776 5 %RANDOM
Rwork0.23822 ---
obs0.24128 33614 98.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.996 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å2-0.06 Å2
2---0.07 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 2.6→46.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6609 0 0 107 6716
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0226770
X-RAY DIFFRACTIONr_angle_refined_deg1.7151.9539195
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5885817
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.06624.164317
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.506151138
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9261539
X-RAY DIFFRACTIONr_chiral_restr0.120.21011
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0215152
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 121 -
Rwork0.312 2360 -
obs--94.41 %

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