+Open data
-Basic information
Entry | Database: PDB / ID: 5hag | ||||||
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Title | Structure of Chlamydia trachomatis effector protein ChlaDUB1 | ||||||
Components | Deubiquitinase and deneddylase Dub1 | ||||||
Keywords | HYDROLASE / Enzyme / CE clan / Deubiquitinase / Acetyltransferase | ||||||
Function / homology | Function and homology information deNEDDylase activity / deSUMOylase activity / protein desumoylation / protein deneddylation / protein deubiquitination / host cell / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / proteolysis / extracellular region / membrane Similarity search - Function | ||||||
Biological species | Chlamydia trachomatis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å | ||||||
Authors | Pruneda, J.N. / Komander, D. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Mol.Cell / Year: 2016 Title: The Molecular Basis for Ubiquitin and Ubiquitin-like Specificities in Bacterial Effector Proteases. Authors: Pruneda, J.N. / Durkin, C.H. / Geurink, P.P. / Ovaa, H. / Santhanam, B. / Holden, D.W. / Komander, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5hag.cif.gz | 70.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5hag.ent.gz | 51.1 KB | Display | PDB format |
PDBx/mmJSON format | 5hag.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ha/5hag ftp://data.pdbj.org/pub/pdb/validation_reports/ha/5hag | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 31307.244 Da / Num. of mol.: 1 / Fragment: UNP residues 130-401 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chlamydia trachomatis (bacteria) / Gene: cdu1, CTL0247 / Production host: Escherichia coli (E. coli) References: UniProt: B0B9A0, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases |
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#2: Chemical | ChemComp-GOL / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.15 Å3/Da / Density % sol: 60.97 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES (pH 7.5), 20% PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 27, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→35.62 Å / Num. obs: 23093 / % possible obs: 99.9 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 2.1→2.16 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.521 / Mean I/σ(I) obs: 2.8 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.1→35.62 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.23 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→35.62 Å
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Refine LS restraints |
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LS refinement shell |
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