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- PDB-5c5z: Crystal structure analysis of c4763, a uropathogenic E. coli-spec... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5c5z | ||||||
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Title | Crystal structure analysis of c4763, a uropathogenic E. coli-specific protein | ||||||
![]() | Glutamyl-tRNA amidotransferase | ||||||
![]() | HYDROLASE / GGCT-like domain / urea / uropathogenic E. coli | ||||||
Function / homology | allophanate hydrolase / allophanate hydrolase activity / Gamma-glutamyl cyclotransferase-like / Hypothetical upf0131 protein ytfp / transferase activity / Roll / Alpha Beta / Allophanate hydrolase![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kim, H. / Choi, J. / Kim, D. / Kim, K.K. | ||||||
![]() | ![]() Title: Crystal structure analysis of c4763, a uropathogenic Escherichia coli-specific protein. Authors: Kim, H. / Choi, J. / Kim, D. / Kim, K.K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 63.2 KB | Display | ![]() |
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PDB format | ![]() | 49.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 430.6 KB | Display | ![]() |
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Full document | ![]() | 432.5 KB | Display | |
Data in XML | ![]() | 13.5 KB | Display | |
Data in CIF | ![]() | 19.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 15632.979 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 42.43 % |
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Crystal grow | Temperature: 295 K / Method: microbatch / pH: 6.2 / Details: PEG 400, NaCl |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Dec 11, 2010 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Redundancy: 28.9 % / Number: 1394843 / Rmerge(I) obs: 0.088 / Χ2: 4.51 / D res high: 1.45 Å / D res low: 30 Å / Num. obs: 48282 / % possible obs: 99.9 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 1.45→30 Å / Num. obs: 48241 / % possible obs: 99.9 % / Redundancy: 14.5 % / Biso Wilson estimate: 13.36 Å2 / Rmerge(I) obs: 0.078 / Χ2: 2.764 / Net I/av σ(I): 64.6 / Net I/σ(I): 14.3 / Num. measured all: 697928 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 66.44 Å2 / Biso mean: 16.42 Å2 / Biso min: 6.97 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.45→24.721 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14
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