+Open data
-Basic information
Entry | Database: PDB / ID: 3oqc | ||||||
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Title | Ubiquitin-fold modifier 1 Specific Protease, UfSP2 | ||||||
Components | Ufm1-specific protease 2 | ||||||
Keywords | HYDROLASE / DPH motif Cys protease | ||||||
Function / homology | Function and homology information deUFMylase activity / thiolester hydrolase activity / regulation of intracellular estrogen receptor signaling pathway / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / endoplasmic reticulum / proteolysis / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 Å | ||||||
Authors | Ha, B.H. / Chung, C.H. / Kim, E.E. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3oqc.cif.gz | 176.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3oqc.ent.gz | 140.1 KB | Display | PDB format |
PDBx/mmJSON format | 3oqc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3oqc_validation.pdf.gz | 447.9 KB | Display | wwPDB validaton report |
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Full document | 3oqc_full_validation.pdf.gz | 482 KB | Display | |
Data in XML | 3oqc_validation.xml.gz | 34.1 KB | Display | |
Data in CIF | 3oqc_validation.cif.gz | 46.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oq/3oqc ftp://data.pdbj.org/pub/pdb/validation_reports/oq/3oqc | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | 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 / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.91 % |
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Crystal grow | Temperature: 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 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 0.97947, 0.979613, 0.97177, 1.0 | |||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 7, 2008 | |||||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.6→46.1 Å / Num. obs: 35942 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 | |||||||||||||||
Reflection shell | Resolution: 2.6→2.69 Å / % possible all: 96.6 |
-Processing
Software |
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Refinement | Method 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
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.996 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→46.1 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.667 Å / Total num. of bins used: 20
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