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Yorodumi- PDB-6trf: Chaetomium thermophilum UDP-Glucose Glucosyl Transferase (UGGT) p... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6trf | ||||||||||||
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Title | Chaetomium thermophilum UDP-Glucose Glucosyl Transferase (UGGT) purified from cells treated with kifunensine. | ||||||||||||
Components | UDP-glucose-glycoprotein glucosyltransferase-like protein | ||||||||||||
Keywords | PROTEIN BINDING / Endoplasmic Reticulum / Glycoprotein Folding / ERQC / kifunensine / UGGT | ||||||||||||
Function / homology | Function and homology information UDP-glucose:glycoprotein glucosyltransferase activity / protein N-linked glycosylation via asparagine / unfolded protein binding / endoplasmic reticulum lumen / nucleotide binding / metal ion binding Similarity search - Function | ||||||||||||
Biological species | Chaetomium thermophilum (fungus) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.106 Å | ||||||||||||
Authors | Roversi, P. / Zitzmann, N. | ||||||||||||
Funding support | United Kingdom, 3items
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Citation | Journal: Structure / Year: 2021 Title: Clamping, bending, and twisting inter-domain motions in the misfold-recognizing portion of UDP-glucose: Glycoprotein glucosyltransferase. Authors: Modenutti, C.P. / Blanco Capurro, J.I. / Ibba, R. / Alonzi, D.S. / Song, M.N. / Vasiljevic, S. / Kumar, A. / Chandran, A.V. / Tax, G. / Marti, L. / Hill, J.C. / Lia, A. / Hensen, M. / ...Authors: Modenutti, C.P. / Blanco Capurro, J.I. / Ibba, R. / Alonzi, D.S. / Song, M.N. / Vasiljevic, S. / Kumar, A. / Chandran, A.V. / Tax, G. / Marti, L. / Hill, J.C. / Lia, A. / Hensen, M. / Waksman, T. / Rushton, J. / Rubichi, S. / Santino, A. / Marti, M.A. / Zitzmann, N. / Roversi, P. #1: Journal: Biorxiv / Year: 2019 Title: Clamping, bending, and twisting inter-domain motions in the misfold-recognising portion of UDP-glucose:glycoprotein glucosyl-transferase Authors: Roversi, P. / Zitzmann, N. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6trf.cif.gz | 527.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6trf.ent.gz | 426.7 KB | Display | PDB format |
PDBx/mmJSON format | 6trf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tr/6trf ftp://data.pdbj.org/pub/pdb/validation_reports/tr/6trf | HTTPS FTP |
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-Related structure data
Related structure data | 6trtC 6ts2C 6ts8C 5nv4S 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 169638.328 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) Gene: CTHT_0048990 / Plasmid: phlsec / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: G0SB58 | ||||
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#2: Polysaccharide | alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D- ...alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||||
#3: Sugar | #4: Chemical | ChemComp-CA / | 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: 3.29 Å3/Da / Density % sol: 62.56 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.03M Sodium nitrate, 0.03 Sodium phosphate dibasic, 0.03M Ammonium sulfate; Tris Bicine pH 8.5; 40% v/v Glycerol, 20% w/v PEG 4000 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: May 1, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 4.106→95.149 Å / Num. obs: 7500 / % possible obs: 90.2 % / Redundancy: 10.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.149 / Rpim(I) all: 0.047 / Rrim(I) all: 0.157 / Net I/σ(I): 9.9 |
Reflection shell | Resolution: 4.106→4.493 Å / Redundancy: 15.9 % / Rmerge(I) obs: 3.268 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 271 / CC1/2: 0.566 / Rpim(I) all: 0.836 / Rrim(I) all: 3.376 / % possible all: 72.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5nv4 Resolution: 4.106→95.149 Å / Cor.coef. Fo:Fc: 0.892 / Cor.coef. Fo:Fc free: 0.824 / Cross valid method: THROUGHOUT / SU Rfree Blow DPI: 2.033 Details: The structure was refined in autoBUSTER with one TLS body per domain, one rigid body per domain, with external restraints to PDB ID 5NV4.
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Displacement parameters | Biso mean: 270.25 Å2
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Refine analyze | Luzzati coordinate error obs: 0.9 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 4.106→95.149 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 4.082→4.62 Å
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Refinement TLS params. | Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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