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Yorodumi- PDB-3qhp: Crystal structure of the catalytic domain of cholesterol-alpha-gl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3qhp | ||||||
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Title | Crystal structure of the catalytic domain of cholesterol-alpha-glucosyltransferase from Helicobacter pylori | ||||||
Components | Type 1 capsular polysaccharide biosynthesis protein J (CapJ) | ||||||
Keywords | TRANSFERASE / Rossmann Fold / glycosyltransferase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Helicobacter pylori (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å | ||||||
Authors | Lee, S.J. / Lee, B.I. / Suh, S.W. | ||||||
Citation | Journal: Proteins / Year: 2011 Title: Crystal structure of the catalytic domain of cholesterol-alpha-glucosyltransferase from Helicobacter pylori Authors: Lee, S.J. / Lee, B.I. / Suh, S.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3qhp.cif.gz | 79.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3qhp.ent.gz | 59.8 KB | Display | PDB format |
PDBx/mmJSON format | 3qhp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3qhp_validation.pdf.gz | 433.5 KB | Display | wwPDB validaton report |
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Full document | 3qhp_full_validation.pdf.gz | 439.3 KB | Display | |
Data in XML | 3qhp_validation.xml.gz | 16.6 KB | Display | |
Data in CIF | 3qhp_validation.cif.gz | 24.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qh/3qhp ftp://data.pdbj.org/pub/pdb/validation_reports/qh/3qhp | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 18578.461 Da / Num. of mol.: 2 / Fragment: catalytic domain, residues 201-366 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: ATCC 26695 / Gene: HP0421 / Plasmid: pET-21a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3)pLysS / References: UniProt: O25175 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40.21 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1M HEPES (pH 7.5), 25% (w/v) PEG 3350, 0.1M glycine, VAPOR DIFFUSION, SITTING DROP, temperature 297K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 1.5→20 Å / Num. obs: 45557 / % possible obs: 96 % | |||||||||||||||
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.141 / Mean I/σ(I) obs: 8.6 / Rsym value: 0.138 / % possible all: 94.3 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.5→19.94 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.933 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 1.368 / SU ML: 0.053 / Cross valid method: THROUGHOUT / ESU R: 0.09 / ESU R Free: 0.089 / 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 max: 51.71 Å2 / Biso mean: 17.49 Å2 / Biso min: 3.55 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→19.94 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.501→1.54 Å / Total num. of bins used: 20
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