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Yorodumi- PDB-6fdu: Structure of Chlamydia trachomatis effector protein Cdu1 bound to... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6fdu | ||||||
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Title | Structure of Chlamydia trachomatis effector protein Cdu1 bound to Compound 3 | ||||||
Components | Deubiquitinase and deneddylase Dub1 | ||||||
Keywords | HYDROLASE / ChlaDUB1 / CE protease / DUB / Ubiquitin / covalent inhibitor. | ||||||
Function / homology | Function and homology information deNEDDylase activity / protein deneddylation / host cell / protein deubiquitination / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / proteolysis / extracellular region / membrane Similarity search - Function | ||||||
Biological species | Chlamydia trachomatis serovar L2 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Ramirez, Y. / Kisker, C. / Altmann, E. | ||||||
Funding support | Germany, 1items
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Citation | Journal: ChemMedChem / Year: 2018 Title: Structural Basis of Substrate Recognition and Covalent Inhibition of Cdu1 from Chlamydia trachomatis. Authors: Ramirez, Y.A. / Adler, T.B. / Altmann, E. / Klemm, T. / Tiesmeyer, C. / Sauer, F. / Kathman, S.G. / Statsyuk, A.V. / Sotriffer, C. / Kisker, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6fdu.cif.gz | 210.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6fdu.ent.gz | 170.9 KB | Display | PDB format |
PDBx/mmJSON format | 6fdu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fd/6fdu ftp://data.pdbj.org/pub/pdb/validation_reports/fd/6fdu | HTTPS FTP |
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-Related structure data
Related structure data | 6fdkC 6fdqC 5b5qS C: citing same article (ref.) S: Starting model for refinement |
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Similar 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 0 / Auth seq-ID: 163 - 400 / Label seq-ID: 28 - 265
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-Components
#1: Protein | Mass: 30534.355 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chlamydia trachomatis serovar L2 (strain 434/Bu / ATCC VR-902B) (bacteria) Gene: cdu1, CTL0247 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: B0B9A0, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases #2: Chemical | #3: Chemical | ChemComp-D5W / ( | #4: 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: 2.51 Å3/Da / Density % sol: 51.09 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop Details: 100 mM Bicine pH 9.0, 10% PEG 20000, 2% 1, 4 dioxane |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 23, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→43.84 Å / Num. obs: 25773 / % possible obs: 99.59 % / Redundancy: 2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.04711 / Rpim(I) all: 0.04711 / Rrim(I) all: 0.06663 / Net I/σ(I): 8.96 |
Reflection shell | Resolution: 2.279→2.3 Å / Redundancy: 2 % / Num. unique obs: 2743 / CC1/2: 0.785 / % possible all: 78.12 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5B5Q Resolution: 2.3→43.84 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.925 / SU B: 17.279 / SU ML: 0.198 / Cross valid method: THROUGHOUT / ESU R: 0.334 / ESU R Free: 0.23 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.361 Å2
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Refinement step | Cycle: 1 / Resolution: 2.3→43.84 Å
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Refine LS restraints |
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