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Yorodumi- PDB-6ts8: Chaetomium thermophilum UDP-Glucose Glucosyl Transferase (UGGT) d... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ts8 | ||||||||||||
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Title | Chaetomium thermophilum UDP-Glucose Glucosyl Transferase (UGGT) double cysteine mutant G177C/A786C. | ||||||||||||
Components | UDP-glucose-glycoprotein glucosyltransferase-like protein | ||||||||||||
Keywords | PROTEIN BINDING / Endoplasmic Reticulum / Glycoprotein Folding / ERQC / UGGT | ||||||||||||
Function / homology | Function and homology information UDP-glucose:glycoprotein glucosyltransferase activity / protein glycosylation / endoplasmic reticulum lumen / metal ion binding Similarity search - Function | ||||||||||||
Biological species | Chaetomium thermophilum (fungus) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.6 Å | ||||||||||||
Authors | Roversi, P. / Zitzmann, N. / Ibba, R. / Hensen, M. / Chandran, A. | ||||||||||||
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. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ts8.cif.gz | 1010.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ts8.ent.gz | 838.1 KB | Display | PDB format |
PDBx/mmJSON format | 6ts8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ts/6ts8 ftp://data.pdbj.org/pub/pdb/validation_reports/ts/6ts8 | HTTPS FTP |
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-Related structure data
Related structure data | 6trfC 6trtC 6ts2C 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: 0 / Auth seq-ID: 28 - 1409 / Label seq-ID: 1 - 1382
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-Components
#1: Protein | Mass: 156354.812 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Chaetomium thermophilum UDP-Glucose Glucosyl Transferase (UGGT) double cysteine mutant G177C/A786C. Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0048990 / Plasmid: pHLsec / Cell (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: G0SB58 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: 2.47 Å3/Da / Density % sol: 50.17 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.8 Details: 16.54% w/v PEG 4,000, 0.03 M citric acid pH 5.3, 0.07 M citric Acid pH 6.0, 12.75% v/v isopropanol |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 8, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 4.59→139.05 Å / Num. obs: 22051 / % possible obs: 87.8 % / Redundancy: 4.3 % / CC1/2: 0.982 / Rmerge(I) obs: 0.278 / Rpim(I) all: 0.147 / Rrim(I) all: 0.316 / Net I/σ(I): 4.6 |
Reflection shell | Resolution: 4.717→5.576 Å / Redundancy: 6.8 % / Rmerge(I) obs: 1.255 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1744 / CC1/2: 0.589 / Rpim(I) all: 0.52 / Rrim(I) all: 1.338 / % possible all: 69.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5nv4 Resolution: 4.6→139.04 Å / Cor.coef. Fo:Fc: 0.892 / Cor.coef. Fo:Fc free: 0.887 / SU B: 258.499 / SU ML: 1.351 / Cross valid method: THROUGHOUT / ESU R Free: 2.993 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 160.355 Å2
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Refinement step | Cycle: 1 / Resolution: 4.6→139.04 Å
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Refine LS restraints |
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