+Open data
-Basic information
Entry | Database: PDB / ID: 7p99 | ||||||
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Title | Structure of human USPL1 in complex with SUMO2 | ||||||
Components |
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Keywords | HYDROLASE / USPL1 / SUMO2 | ||||||
Function / homology | Function and homology information snRNA transcription / Cajal body organization / deSUMOylase activity / protein desumoylation / SUMO binding / Cajal body / cell population proliferation / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / proteolysis / extracellular space / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Peromyscus maniculatus bairdii (prairie deer mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Reverter, D. / Ying, L. | ||||||
Funding support | Spain, 1items
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Citation | Journal: Nat Commun / Year: 2022 Title: Structural basis for the SUMO protease activity of the atypical ubiquitin-specific protease USPL1. Authors: Li, Y. / Varejao, N. / Reverter, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7p99.cif.gz | 161.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7p99.ent.gz | 123.2 KB | Display | PDB format |
PDBx/mmJSON format | 7p99.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p9/7p99 ftp://data.pdbj.org/pub/pdb/validation_reports/p9/7p99 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 38686.297 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: USPL1, C13orf22, D13S106 / Production host: Escherichia coli (E. coli) References: UniProt: Q5W0Q7, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases |
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#2: Protein | Mass: 11494.796 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Point mutant C54S and G93A Source: (gene. exp.) Peromyscus maniculatus bairdii (prairie deer mouse) Gene: Sumo2 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6J0CIQ7 |
#3: Chemical | ChemComp-ZN / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.89 Å3/Da / Density % sol: 35.05 % |
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Crystal grow | Temperature: 311 K / Method: vapor diffusion, hanging drop Details: 0.2M Potassium thiocyanate, 0.1M Sodium Acetate pH 5.0, 8% PEG20000, 8% PEG500MME |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9762 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 23, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 1.799→41.041 Å / Num. obs: 33606 / % possible obs: 96.5 % / Redundancy: 2.5 % / CC1/2: 0.993 / Net I/σ(I): 7.8 |
Reflection shell | Resolution: 1.799→1.83 Å / Num. unique obs: 1664 / CC1/2: 0.978 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: ALPHAFOLD Resolution: 1.8→41.04 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 20.49 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 81.67 Å2 / Biso mean: 33.986 Å2 / Biso min: 14.14 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.8→41.04 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12
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Refinement TLS params. | Method: refined / Origin x: 19.3362 Å / Origin y: 7.6516 Å / Origin z: -1.9001 Å
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Refinement TLS group |
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