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- PDB-6fdu: Structure of Chlamydia trachomatis effector protein Cdu1 bound to... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6fdu | ||||||
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Title | Structure of Chlamydia trachomatis effector protein Cdu1 bound to Compound 3 | ||||||
![]() | Deubiquitinase and deneddylase Dub1 | ||||||
![]() | HYDROLASE / ChlaDUB1 / CE protease / DUB / Ubiquitin / covalent inhibitor. | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ramirez, Y. / Kisker, C. / Altmann, E. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 210.4 KB | Display | ![]() |
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PDB format | ![]() | 170.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6fdkC ![]() 6fdqC ![]() 5b5qS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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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: _ / 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: _ / 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.) ![]() Gene: cdu1, CTL0247 Production host: ![]() ![]() 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: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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