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- PDB-1ef2: CRYSTAL STRUCTURE OF MANGANESE-SUBSTITUTED KLEBSIELLA AEROGENES UREASE -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ef2 | ||||||
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Title | CRYSTAL STRUCTURE OF MANGANESE-SUBSTITUTED KLEBSIELLA AEROGENES UREASE | ||||||
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![]() | HYDROLASE / alpha-beta barrel / metalloenzyme | ||||||
Function / homology | ![]() urease complex / urease / urease activity / urea catabolic process / nickel cation binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() | ||||||
![]() | Yamaguchi, K. / Cosper, N.J. / Stalhandske, C. / Scott, R.A. / Pearson, M.A. / Karplus, P.A. / Hausinger, R.P. | ||||||
![]() | ![]() Title: Characterization of metal-substituted Klebsiella aerogenes urease. Authors: Yamaguchi, K. / Cosper, N.J. / Stalhandske, C. / Scott, R.A. / Pearson, M.A. / Karplus, P.A. / Hausinger, R.P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 153.9 KB | Display | ![]() |
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PDB format | ![]() | 126.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 433.9 KB | Display | ![]() |
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Full document | ![]() | 439.5 KB | Display | |
Data in XML | ![]() | 28.9 KB | Display | |
Data in CIF | ![]() | 40.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
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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: 60278.164 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||
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#2: Protein | Mass: 11125.690 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||
#3: Protein | Mass: 11100.928 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.09 % | ||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: lithium sulfate, HEPES, EDTA, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||
Crystal | *PLUS Density % sol: 49 % | ||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ![]() |
Detector | Type: ADSC / Detector: AREA DETECTOR |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→100 Å / Num. obs: 27559 / % possible obs: 99 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.108 |
Reflection shell | Resolution: 2.5→2.59 Å / Rmerge(I) obs: 0.322 |
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Processing
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Refinement | Resolution: 2.5→10 Å / Rfactor Rwork: 0.172 / σ(F): 0 / Stereochemistry target values: Engh and Huber | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→10 Å
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Software | *PLUS Name: ![]() | ||||||||||||||||||||
Refine LS restraints | *PLUS
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