+Open data
-Basic information
Entry | Database: PDB / ID: 2xgo | ||||||
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Title | XcOGT in complex with UDP-S-GlcNAc | ||||||
Components | XCOGT | ||||||
Keywords | TRANSFERASE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | XANTHOMONAS CAMPESTRIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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 | 2xgo.cif.gz | 209.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xgo.ent.gz | 166.7 KB | Display | PDB format |
PDBx/mmJSON format | 2xgo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xg/2xgo ftp://data.pdbj.org/pub/pdb/validation_reports/xg/2xgo | HTTPS FTP |
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-Related structure data
Related structure data | 2xgmC 2xgsC 2jlbS 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: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: 1 / Auth seq-ID: 28 - 568 / Label seq-ID: 28 - 568
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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 | ChemComp-ZKD / | #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: 0.1 M CHES, PH 9.5, 25% POLYETHYLENEGLYCOL 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→30 Å / Num. obs: 37400 / % possible obs: 91.7 % / Observed criterion σ(I): 2 / Redundancy: 4.9 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 32.5 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 2.9 / % possible all: 86.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2JLB Resolution: 2.6→19.84 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.896 / SU B: 39.342 / SU ML: 0.399 / Cross valid method: THROUGHOUT / ESU R: 1.113 / ESU R Free: 0.387 / 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: 49.62 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→19.84 Å
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Refine LS restraints |
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