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Yorodumi- PDB-2xgm: Substrate and product analogues as human O-GlcNAc transferase inh... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2xgm | ||||||
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Title | Substrate and product analogues as human O-GlcNAc transferase inhibitors. | ||||||
Components | XCOGT | ||||||
Keywords | TRANSFERASE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | XANTHOMONAS CAMPESTRIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.55 Å | ||||||
Authors | Dorfmueller, H.C. / Borodkin, V.S. / Blair, D.E. / Pathak, S. / Navratilova, I. / van Aalten, D.M. | ||||||
Citation | Journal: Amino Acids / Year: 2011 Title: Substrate and Product Analogues as Human O-Glcnac Transferase Inhibitors. Authors: Dorfmueller, H.C. / Borodkin, V.S. / Blair, D.E. / Pathak, S. / Navratilova, I. / Van Aalten, D.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2xgm.cif.gz | 197.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xgm.ent.gz | 165.8 KB | Display | PDB format |
PDBx/mmJSON format | 2xgm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xg/2xgm ftp://data.pdbj.org/pub/pdb/validation_reports/xg/2xgm | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
#1: Protein | Mass: 61424.688 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) XANTHOMONAS CAMPESTRIS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) PLYSS / References: UniProt: Q8PC69 #2: Chemical | #3: Water | ChemComp-HOH / | |
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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: 2.25 Å3/Da / Density % sol: 45 % / Description: NONE |
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Crystal grow | Details: 0.1MCHES, PH 9.5, 25% POLYETHYLENEGLYCOL 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.5 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→20 Å / Num. obs: 42658 / % possible obs: 97.8 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 16.3 |
-Processing
Software | Name: REFMAC / Version: 5.5.0109 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: OTHER Starting model: NONE Resolution: 2.55→20 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.906 / SU B: 38.921 / SU ML: 0.408 / Cross valid method: THROUGHOUT / ESU R: 0.66 / ESU R Free: 0.353 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.62 Å2
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Refinement step | Cycle: LAST / Resolution: 2.55→20 Å
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Refine LS restraints |
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