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Yorodumi- PDB-6yv9: Mannosyltransferase PcManGT from Pyrobaculum calidifontis in comp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6yv9 | ||||||||||||
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Title | Mannosyltransferase PcManGT from Pyrobaculum calidifontis in complex with GDP-Man and Mn2+ | ||||||||||||
Components | (Glycosyl transferase, family 2Glycosyltransferase) x 2 | ||||||||||||
Keywords | TRANSFERASE / Glycosyltransferase / Membrane protein / Mannosyltransferase / GDP-mannose | ||||||||||||
Function / homology | Glycosyltransferase 2-like / Glycosyl transferase family 2 / Nucleotide-diphospho-sugar transferases / transferase activity / GUANOSINE-5'-DIPHOSPHATE-ALPHA-D-MANNOSE / : / Glycosyl transferase, family 2 Function and homology information | ||||||||||||
Biological species | Pyrobaculum calidifontis (archaea) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.7 Å | ||||||||||||
Authors | Divne, C. / Gandini, R. | ||||||||||||
Funding support | Sweden, 3items
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Citation | Journal: J.Mol.Biol. / Year: 2020 Title: A Transmembrane Crenarchaeal Mannosyltransferase Is Involved in N-Glycan Biosynthesis and Displays an Unexpected Minimal Cellulose-Synthase-like Fold. Authors: Gandini, R. / Reichenbach, T. / Spadiut, O. / Tan, T.C. / Kalyani, D.C. / Divne, C. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6yv9.cif.gz | 283 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6yv9.ent.gz | 237 KB | Display | PDB format |
PDBx/mmJSON format | 6yv9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yv/6yv9 ftp://data.pdbj.org/pub/pdb/validation_reports/yv/6yv9 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 38978.641 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrobaculum calidifontis (strain JCM 11548 / VA1) (archaea) Strain: JCM 11548 / VA1 / Gene: Pcal_0472 / Plasmid: Plasmid / Details (production host): pWaldo-GFPd / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A3MTD6 | ||||
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#2: Protein | Mass: 39109.836 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrobaculum calidifontis (strain JCM 11548 / VA1) (archaea) Strain: JCM 11548 / VA1 / Gene: Pcal_0472 / Plasmid: Plasmid / Details (production host): pWaldo-GFPd / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A3MTD6 | ||||
#3: Chemical | #4: Chemical | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 50 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1 mM HEPES (pH 7.5), 20% PEG 4000, 10% isopropanol, 10 mM MnCl2 and 2% 1,2,3-heptanetriol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.95 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 7, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→49.1 Å / Num. obs: 25613 / % possible obs: 99.5 % / Redundancy: 12.5 % / CC1/2: 0.999 / Net I/σ(I): 16.3 |
Reflection shell | Resolution: 2.7→2.8 Å / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2547 / CC1/2: 0.799 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 2.7→46.413 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 31.6
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→46.413 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.7675 Å
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