+Open data
-Basic information
Entry | Database: PDB / ID: 5ham | ||||||
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Title | Structure of Rickettsia bellii effector protein RickCE | ||||||
Components | RickCE | ||||||
Keywords | HYDROLASE / Enzyme / CE clan / Deubiquitinase | ||||||
Function / homology | Papain-like cysteine peptidase superfamily / Uncharacterized protein Function and homology information | ||||||
Biological species | Rickettsia bellii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 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 | 5ham.cif.gz | 215.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ham.ent.gz | 172.7 KB | Display | PDB format |
PDBx/mmJSON format | 5ham.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ha/5ham ftp://data.pdbj.org/pub/pdb/validation_reports/ha/5ham | HTTPS FTP |
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-Related structure data
-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: 31104.229 Da / Num. of mol.: 2 / Fragment: UNP residues 420-691 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rickettsia bellii (bacteria) / Gene: RBE_0198 / Production host: Escherichia coli (E. coli) / References: UniProt: Q1RK35 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.42 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Tris (pH 7.5), 2 M Ammonium citrate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9174 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 3, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9174 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→52.08 Å / Num. obs: 24203 / % possible obs: 99.2 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 2.4→2.49 Å / Rmerge(I) obs: 0.596 / Mean I/σ(I) obs: 2 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.4→52.075 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 23.76 / 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: 2.4→52.075 Å
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Refine LS restraints |
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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 |
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