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- PDB-4ri1: Crystal structure of Helicobacter pylori pseudaminic acid biosynt... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4ri1 | ||||||
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Title | Crystal structure of Helicobacter pylori pseudaminic acid biosynthesis N -acetyltransferase PseH complex with acetyl-coA | ||||||
![]() | UDP-4-amino-4,6-dideoxy-N-acetyl-beta-L-altrosamine N-acetyltransferase | ||||||
![]() | TRANSFERASE / GNAT family / N-acetyl transferase / acetyl-CoA / none | ||||||
Function / homology | ![]() UDP-4-amino-4,6-dideoxy-N-acetyl-beta-L-altrosamine N-acetyltransferase / N-acetyltransferase activity Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Roujeinikova, A. / Ud-Din, A.I. | ||||||
![]() | ![]() Title: Crystal Structure of Helicobacter pylori Pseudaminic Acid Biosynthesis N-Acetyltransferase PseH: Implications for Substrate Specificity and Catalysis. Authors: Ud-Din, A.I. / Liu, Y.C. / Roujeinikova, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 130.2 KB | Display | ![]() |
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PDB format | ![]() | 103.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 25.8 KB | Display | |
Data in CIF | ![]() | 34.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 22015.268 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: O25094, UDP-4-amino-4,6-dideoxy-N-acetyl-beta-L-altrosamine N-acetyltransferase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.94 Å3/Da / Density % sol: 75.1 % |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 4.2 Details: 0.9 M diammonium tartrate, 80 mM sodium acetate trihydrate pH 4.2, 3 mM acetyl-CoA, VAPOR DIFFUSION, HANGING DROP, temperature 2930.9 M diammonium tartrate, 80 mM sodium acetate trihydrate ...Details: 0.9 M diammonium tartrate, 80 mM sodium acetate trihydrate pH 4.2, 3 mM acetyl-CoA, VAPOR DIFFUSION, HANGING DROP, temperature 2930.9 M diammonium tartrate, 80 mM sodium acetate trihydrate pH 4.2 and acetyl-CoA at a concentration of 3 mMK |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→40 Å / Num. obs: 54332 / % possible obs: 93.8 % / Observed criterion σ(F): 168694 / Observed criterion σ(I): 168694 |
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Processing
Software | Name: PHENIX / Version: (phenix.refine: 1.9_1692) / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: AB INITIO PHASING / Resolution: 2.3→29.989 Å / SU ML: 0.31 / σ(F): 1.34 / Phase error: 23.61 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→29.989 Å
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Refine LS restraints |
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LS refinement shell |
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