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- PDB-8bpd: Structural and Functional Characterization of the Novel Endo-alph... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8bpd | ||||||
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Title | Structural and Functional Characterization of the Novel Endo-alpha(1,4)-Fucoidanase Mef1 from the Marine Bacterium Muricauda eckloniae | ||||||
![]() | Glycosyl hydrolase | ||||||
![]() | HYDROLASE / Fucoidanase / Fucoidan / GH107 / glycosyl hydrolase / Fucanase / calcium binding / polysaccharide / sulfated. | ||||||
Function / homology | Chem-3CX / Uncharacterized protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Mikkelsen, M.D. / Meyer, A.S. / Morth, J.P. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural and functional characterization of the novel endo-alpha (1,4)-fucoidanase Mef1 from the marine bacterium Muricauda eckloniae. Authors: Mikkelsen, M.D. / Tran, V.H.N. / Meier, S. / Nguyen, T.T. / Holck, J. / Cao, H.T.T. / Van, T.T.T. / Thinh, P.D. / Meyer, A.S. / Morth, J.P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 280.9 KB | Display | ![]() |
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PDB format | ![]() | 188.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 19.3 KB | Display | |
Data in CIF | ![]() | 29.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6m8nS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 45088.668 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||||||
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#2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.78 Å3/Da / Density % sol: 55.81 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 24 % PEG 3350, 0.1 M CAPSO pH 9, 3 % isopropanol, 4 % PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 24, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→43.72 Å / Num. obs: 45842 / % possible obs: 99.87 % / Redundancy: 6.8 % / Biso Wilson estimate: 25.27 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.1267 / Rpim(I) all: 0.05163 / Rrim(I) all: 0.1369 / Net I/σ(I): 6.8 |
Reflection shell | Resolution: 1.8→1.864 Å / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 0.48 / Num. unique obs: 4540 / CC1/2: 0.833 / CC star: 0.953 / Rpim(I) all: 0.4176 / Rrim(I) all: 1 / % possible all: 99.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6M8N Resolution: 1.8→43.72 Å / SU ML: 0.2742 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.7185 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.58 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→43.72 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 | Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A
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