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Open data
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Basic information
Entry | Database: PDB / ID: 1e9z | ||||||
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Title | Crystal structure of Helicobacter pylori urease | ||||||
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![]() | HYDROLASE | ||||||
Function / homology | ![]() urease complex / urease / urease activity / urea catabolic process / nickel cation binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Ha, N.-C. / Oh, S.-T. / Oh, B.-H. | ||||||
![]() | ![]() Title: Supramolecular Assembly and Acid Resistance of Helicobacter Pylori Urease Authors: Ha, N.-C. / Oh, S.-T. / Sung, J.Y. / Cha, K.-A. / Hyung Lee, M. / Oh, B.-H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 166.8 KB | Display | ![]() |
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PDB format | ![]() | 130.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 437.4 KB | Display | ![]() |
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Full document | ![]() | 496.3 KB | Display | |
Data in XML | ![]() | 37.2 KB | Display | |
Data in CIF | ![]() | 51.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1e9yC ![]() 1kau C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 26571.662 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||
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#2: Protein | Mass: 61745.422 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 51 % | ||||||||||||||||||||
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Crystal grow | pH: 6.5 / Details: pH 6.50 | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 12 ℃ / Method: vapor diffusion, hanging drop / Details: used macroseeding | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MACSCIENCE / Detector: IMAGE PLATE |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3→20 Å / Num. obs: 21702 / % possible obs: 95.3 % / Observed criterion σ(I): 1 / Redundancy: 20 % / Rmerge(I) obs: 0.115 / Rsym value: 0.115 / Net I/σ(I): 5.7 |
Reflection | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 20 Å / Num. obs: 23292 / % possible obs: 89.1 % / Num. measured all: 393095 / Rmerge(I) obs: 0.114 |
Reflection shell | *PLUS % possible obs: 75.8 % / Rmerge(I) obs: 0.317 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1KAU ![]() 1kau Resolution: 3→20 Å / Cross valid method: THROUGHOUT / σ(F): 1
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Refinement step | Cycle: LAST / Resolution: 3→20 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 40 Å / σ(F): 1 / Rfactor obs: 0.206 / Rfactor Rfree: 0.287 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |