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Yorodumi- PDB-6ry2: Crystal structure of Dfg5 from Chaetomium thermophilum in complex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ry2 | ||||||
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Title | Crystal structure of Dfg5 from Chaetomium thermophilum in complex with alpha-1,2-mannobiose | ||||||
Components | Mannan endo-1,6-alpha-mannosidase | ||||||
Keywords | HYDROLASE / Transglycosidase / Fungal Cell Wall / Plasma Membrane / GPI-anchor / GPI-CWP | ||||||
Function / homology | Function and homology information mannan endo-1,6-alpha-mannosidase / mannan endo-1,6-alpha-mannosidase activity / carbohydrate catabolic process / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Chaetomium thermophilum (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å | ||||||
Authors | Essen, L.-O. / Vogt, M.S. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2020 Title: Structural base for the transfer of GPI-anchored glycoproteins into fungal cell walls. Authors: Vogt, M.S. / Schmitz, G.F. / Varon Silva, D. / Mosch, H.U. / Essen, L.O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ry2.cif.gz | 276.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ry2.ent.gz | 234.7 KB | Display | PDB format |
PDBx/mmJSON format | 6ry2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ry2_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6ry2_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6ry2_validation.xml.gz | 24.1 KB | Display | |
Data in CIF | 6ry2_validation.cif.gz | 38.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ry/6ry2 ftp://data.pdbj.org/pub/pdb/validation_reports/ry/6ry2 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein / Sugars , 2 types, 3 molecules A
#1: Protein | Mass: 49546.172 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0020800 / Production host: Escherichia coli B (bacteria) / Strain (production host): SHuffle T7 Express Competent References: UniProt: G0S3F2, mannan endo-1,6-alpha-mannosidase |
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#5: Sugar |
-Non-polymers , 4 types, 666 molecules
#2: Chemical | ChemComp-ACT / | ||||
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#3: Chemical | #4: Chemical | ChemComp-PGE / | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 38.61 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 6 Details: Ammoniumiodide, PEG3350, Calcium acetate, MES, PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.972 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 22, 2018 / Details: Toroidal mirror |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.972 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→41.93 Å / Num. obs: 84221 / % possible obs: 94.32 % / Redundancy: 1.9 % / Biso Wilson estimate: 10.59 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.06 / Rrim(I) all: 0.019 / Net I/σ(I): 8.63 |
Reflection shell | Resolution: 1.3→1.346 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.116 / Mean I/σ(I) obs: 6.01 / Num. unique obs: 8154 / CC1/2: 0.947 / % possible all: 91.56 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→41.856 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 11.04
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.3→41.856 Å
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Refine LS restraints |
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LS refinement shell |
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