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Yorodumi- PDB-8cmr: Linear specific OTU-type DUB SnOTU from the pathogen S. negenvens... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8cmr | |||||||||
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Title | Linear specific OTU-type DUB SnOTU from the pathogen S. negenvensis in complex with linear di-ubiquitin | |||||||||
Components |
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Keywords | HYDROLASE / Deubiquitinase / papain-fold / OTU / swapped complex | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Simkania negevensis Z (bacteria) Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 Å | |||||||||
Authors | Uthoff, M. / Hermanns, T. / Boll, V. / Hofmann, K. / Baumann, U. | |||||||||
Funding support | Germany, 2items
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Citation | Journal: Nat Commun / Year: 2023 Title: Functional and structural diversity in deubiquitinases of the Chlamydia-like bacterium Simkania negevensis. Authors: Boll, V. / Hermanns, T. / Uthoff, M. / Erven, I. / Horner, E.M. / Kozjak-Pavlovic, V. / Baumann, U. / Hofmann, K. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8cmr.cif.gz | 552 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8cmr.ent.gz | 384.6 KB | Display | PDB format |
PDBx/mmJSON format | 8cmr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8cmr_validation.pdf.gz | 437.3 KB | Display | wwPDB validaton report |
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Full document | 8cmr_full_validation.pdf.gz | 438.7 KB | Display | |
Data in XML | 8cmr_validation.xml.gz | 27.2 KB | Display | |
Data in CIF | 8cmr_validation.cif.gz | 37.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cm/8cmr ftp://data.pdbj.org/pub/pdb/validation_reports/cm/8cmr | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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-Components
#1: Protein | Mass: 33878.930 Da / Num. of mol.: 2 / Mutation: C82A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Simkania negevensis Z (bacteria) / Gene: SNE_A17630 / Plasmid: popinS / Production host: Escherichia coli (E. coli) / References: UniProt: F8L9T9 #2: Protein | Mass: 17135.654 Da / Num. of mol.: 2 Fragment: In the crystal structure there is domain swapping likely occurring. The two ubiquitin units of chains B or D are spread over two DUB molecules (A or C). A biological assembly, for example, ...Fragment: In the crystal structure there is domain swapping likely occurring. The two ubiquitin units of chains B or D are spread over two DUB molecules (A or C). A biological assembly, for example, would more likely be Chain A/Chain B:77-152 linked via peptide bond from B152 to D1 to chain D, residues 1-76. Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli (E. coli) / References: UniProt: B4DV12 #3: 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: 2.77 Å3/Da / Density % sol: 55.66 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: The proteins were purified in 20 mM TRIS pH 7.5, 150 mM NaCl, 2mM DTT and mixed in a 1:1.1 (Protease:ubiquitin) ratio. Reservoir: 0.2 M Magnesium format dihydrate, 20 % w/v PEG 3350, 0.02 M ...Details: The proteins were purified in 20 mM TRIS pH 7.5, 150 mM NaCl, 2mM DTT and mixed in a 1:1.1 (Protease:ubiquitin) ratio. Reservoir: 0.2 M Magnesium format dihydrate, 20 % w/v PEG 3350, 0.02 M EDTA Protein and reservoir were mixed in a ratio of 1 ul : 2 ul. Temp details: Climate controlled room |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 16, 2021 |
Radiation | Monochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.24→80 Å / Num. obs: 53800 / % possible obs: 99.9 % / Redundancy: 11.2 % / Biso Wilson estimate: 57.15 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.134 / Rpim(I) all: 0.0417 / Rrim(I) all: 0.1406 / Net I/σ(I): 8.9 |
Reflection shell | Resolution: 2.24→2.32 Å / Redundancy: 11.7 % / Rmerge(I) obs: 1.972 / Num. unique obs: 5272 / CC1/2: 0.643 / Rpim(I) all: 0.6039 / Rrim(I) all: 2.072 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: AlphaFold2; custom version (https://github.com/muthoff/ComplexFold) Resolution: 2.24→43.06 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.8778 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 65.88 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.24→43.06 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION
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