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Yorodumi- PDB-7boo: Crystal Structure of Core-mannan synthase A (CmsA/Ktr4) from Aspe... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7boo | ||||||
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Title | Crystal Structure of Core-mannan synthase A (CmsA/Ktr4) from Aspergillus fumigatus, apo form | ||||||
Components | Alpha-1,2-mannosyltransferase (Ktr4), putative | ||||||
Keywords | TRANSFERASE / Mannosyltransferase | ||||||
Function / homology | Function and homology information mannosyltransferase activity / sporulation / anatomical structure development / protein glycosylation / cell differentiation / membrane Similarity search - Function | ||||||
Biological species | Neosartorya fumigata (mold) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Hira, D. / Onoue, T. / Oka, T. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2020 Title: Structural basis for the core-mannan biosynthesis of cell wall fungal-type galactomannan in Aspergillus fumigatus . Authors: Hira, D. / Onoue, T. / Oka, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7boo.cif.gz | 503.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7boo.ent.gz | 412.8 KB | Display | PDB format |
PDBx/mmJSON format | 7boo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7boo_validation.pdf.gz | 495.4 KB | Display | wwPDB validaton report |
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Full document | 7boo_full_validation.pdf.gz | 515.9 KB | Display | |
Data in XML | 7boo_validation.xml.gz | 94.6 KB | Display | |
Data in CIF | 7boo_validation.cif.gz | 138.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bo/7boo ftp://data.pdbj.org/pub/pdb/validation_reports/bo/7boo | HTTPS FTP |
-Related structure data
Related structure data | 7bopC 5a07S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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: 45301.371 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neosartorya fumigata (strain CEA10 / CBS 144.89 / FGSC A1163) (mold) Strain: CEA10 / CBS 144.89 / FGSC A1163 / Gene: AFUB_051270 / Production host: Escherichia coli (E. coli) / References: UniProt: B0Y2F5 #2: Chemical | ChemComp-NA / #3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 3.78 Å3/Da / Density % sol: 67.5 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / Details: sodium citrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 20, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→45.99 Å / Num. obs: 284394 / % possible obs: 99.79 % / Redundancy: 7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.062 / Rrim(I) all: 0.067 / Net I/σ(I): 19.22 |
Reflection shell | Resolution: 1.95→2.02 Å / Rmerge(I) obs: 0.555 / Mean I/σ(I) obs: 3.38 / Num. unique obs: 27979 / CC1/2: 0.897 / Rrim(I) all: 0.6 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5a07 Resolution: 1.95→45.99 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.962 / SU B: 2.578 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.107 / ESU R Free: 0.102 / 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: 35.973 Å2
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Refinement step | Cycle: 1 / Resolution: 1.95→45.99 Å
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Refine LS restraints |
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