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Yorodumi- PDB-8bpd: Structural and Functional Characterization of the Novel Endo-alph... -
+Open data
-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 | ||||||
Components | Glycosyl hydrolaseGlycoside hydrolase | ||||||
Keywords | HYDROLASE / Fucoidanase / Fucoidan / GH107 / glycosyl hydrolase / Fucanase / calcium binding / polysaccharide / sulfated. | ||||||
Function / homology | Chem-3CX / Uncharacterized protein Function and homology information | ||||||
Biological species | Muricauda eckloniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Mikkelsen, M.D. / Meyer, A.S. / Morth, J.P. | ||||||
Funding support | Denmark, 1items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2023 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8bpd.cif.gz | 280.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8bpd.ent.gz | 188.3 KB | Display | PDB format |
PDBx/mmJSON format | 8bpd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bp/8bpd ftp://data.pdbj.org/pub/pdb/validation_reports/bp/8bpd | HTTPS FTP |
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-Related structure data
Related structure data | 6m8nS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Muricauda eckloniae (bacteria) / Gene: AAY42_01290 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0N8WFH1, EC: 3.2.1.212 | ||||||||
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#2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.9786 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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