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- PDB-5oq2: Se-SAD structure of the functional region of Cwp19 from Clostridi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5oq2 | ||||||
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Title | Se-SAD structure of the functional region of Cwp19 from Clostridium difficile | ||||||
![]() | Cwp19 | ||||||
![]() | HYDROLASE / S-layer / glycoside hydrolase / TIM barrel | ||||||
Function / homology | Glycosyl hydrolase-like 10 / Glycosyl hydrolase-like 10 / Putative cell wall binding repeat 2 / Cell wall binding domain 2 (CWB2) / N-acetylmuramoyl-L-alanine amidase activity / Glycoside hydrolase superfamily / PHOSPHATE ION / Cwp19![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bradshaw, W.J. / Kirby, J.M. / Roberts, A.K. / Shone, C.C. / Acharya, K.R. | ||||||
Funding support | 1items
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![]() | ![]() Title: The molecular structure of the glycoside hydrolase domain of Cwp19 from Clostridium difficile. Authors: Bradshaw, W.J. / Kirby, J.M. / Roberts, A.K. / Shone, C.C. / Acharya, K.R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 154 KB | Display | ![]() |
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PDB format | ![]() | 125.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 457.6 KB | Display | ![]() |
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Full document | ![]() | 459.5 KB | Display | |
Data in XML | ![]() | 26.4 KB | Display | |
Data in CIF | ![]() | 37 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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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Components
#1: Protein | Mass: 45117.457 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: lytC_21, cwp19, lytC_5, SAMEA3374989_00994, SAMEA3375004_02322 Production host: ![]() ![]() References: UniProt: L7PGA3, N-acetylmuramoyl-L-alanine amidase #2: Chemical | #3: Chemical | ChemComp-EDO / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.98 Å3/Da / Density % sol: 38.06 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop Details: 90% (50 mM monobasic potassium phosphate, 14% PEG 8000) 10% (20 mM xylitol, 20 mM myo-inositol, 20 mM D-fructose, 20 mM L-rhammnose monohydrate, 20 mM D-sorbitol, 100 mM BES/TEA pH 7.5, 40% pentane-1,5,-diol) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 15, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→55.13 Å / Num. obs: 30986 / % possible obs: 100 % / Redundancy: 52.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.255 / Rpim(I) all: 0.05 / Rrim(I) all: 0.26 / Net I/σ(I): 28.2 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 53.6 % / Rmerge(I) obs: 0.591 / Mean I/σ(I) obs: 9.9 / Num. unique obs: 3026 / CC1/2: 0.98 / Rpim(I) all: 0.116 / Rrim(I) all: 0.603 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.582 Å2
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Refinement step | Cycle: 1 / Resolution: 2.3→55.13 Å
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Refine LS restraints |
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