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Open data
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Basic information
Entry | Database: PDB / ID: 5noa | |||||||||
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Title | Polysaccharide Lyase BACCELL_00875 | |||||||||
![]() | Family 88 glycosyl hydrolase | |||||||||
![]() | HYDROLASE / Human Gut Microbiota / Polysaccharide lyase / Bacteroides thetaiotaomicron / Gum Arabic | |||||||||
Function / homology | ![]() unsaturated rhamnogalacturonyl hydrolase activity / carbohydrate metabolic process / hydrolase activity Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Cartmell, A. / Munoz-Munoz, J. / Terrapon, N. / Basle, A. / Henrissat, B. / Gilbert, H.J. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: An evolutionarily distinct family of polysaccharide lyases removes rhamnose capping of complex arabinogalactan proteins. Authors: Munoz-Munoz, J. / Cartmell, A. / Terrapon, N. / Basle, A. / Henrissat, B. / Gilbert, H.J. #1: ![]() Title: Rhamnose Capping in Complex Arabinogalactan Proteins Authors: Munoz-Munoz, J. / Cartmell, A. / Terrapon, N. / Basle, A. / Henrissat, B. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 165.8 KB | Display | ![]() |
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PDB format | ![]() | 130.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 413.5 KB | Display | ![]() |
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Full document | ![]() | 413.8 KB | Display | |
Data in XML | ![]() | 16.5 KB | Display | |
Data in CIF | ![]() | 25.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5no8C ![]() 5nokC ![]() 4ce7S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 43673.027 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: yteR_9, BJP75_03260, Btheta7330_04609 / Production host: ![]() ![]() References: UniProt: A0A0P0FFM3, UniProt: Q8A1H4*PLUS, unsaturated rhamnogalacturonyl hydrolase |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.86 Å3/Da / Density % sol: 33.81 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: 200 mM sodium malonate 20% polyethylene glycol (PEG) 3350. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 24, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9798 Å / Relative weight: 1 |
Reflection | Resolution: 1.26→21.13 Å / Num. obs: 87238 / % possible obs: 99.5 % / Redundancy: 8.8 % / CC1/2: 0.998 / Net I/σ(I): 13 |
Reflection shell | Resolution: 1.26→1.28 Å / Redundancy: 3.9 % / Num. unique obs: 4048 / CC1/2: 0.524 / % possible all: 94.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4CE7 Resolution: 1.26→21.13 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.976 / SU B: 1.167 / SU ML: 0.023 / Cross valid method: THROUGHOUT / ESU R: 0.039 / ESU R Free: 0.038 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.271 Å2
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Refinement step | Cycle: 1 / Resolution: 1.26→21.13 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.26→1.293 Å / Total num. of bins used: 20
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