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Open data
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Basic information
Entry | Database: PDB / ID: 8hfd | ||||||
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Title | Crystal structure of allantoinase from E. coli BL21 | ||||||
![]() | Allantoinase | ||||||
![]() | HYDROLASE / allantoinase / allantoin | ||||||
Function / homology | ![]() allantoinase / allantoinase activity / allantoin catabolic process / cobalt ion binding / purine nucleobase metabolic process / zinc ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lin, E.S. / Huang, H.Y. / Yang, P.C. / Liu, H.W. / Huang, C.Y. | ||||||
Funding support | 1items
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![]() | ![]() Title: Crystal Structure of Allantoinase from Escherichia coli BL21: A Molecular Insight into a Role of the Active Site Loops in Catalysis. Authors: Huang, Y.H. / Yang, P.C. / Lin, E.S. / Ho, Y.Y. / Peng, W.F. / Lu, H.P. / Huang, C.C. / Huang, C.Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 367.3 KB | Display | ![]() |
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PDB format | ![]() | 296.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 4.5 MB | Display | ![]() |
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Full document | ![]() | 4.5 MB | Display | |
Data in XML | ![]() | 75.1 KB | Display | |
Data in CIF | ![]() | 105.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3e74S S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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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: 50560.305 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: allB, BMT91_19075, E2127_17875, E2128_18450, E2132_17365, E4T14_14655, E6D34_22765, ELT21_17110 Production host: ![]() ![]() #2: Chemical | ChemComp-PEG / #3: Chemical | ChemComp-ZN / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.81 Å3/Da / Density % sol: 56.3 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9.5 / Details: 20% PEG8000, 100 mM CHES, pH9.5 |
-Data collection
Diffraction | Mean temperature: 298 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Aug 19, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.07→30 Å / Num. obs: 132819 / % possible obs: 99.02 % / Redundancy: 3.5 % / CC1/2: 0.992 / Net I/σ(I): 7.39 |
Reflection shell | Resolution: 2.07→2.19 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 2.14 / Num. unique obs: 12965 / CC1/2: 0.855 / % possible all: 97.21 |
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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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.07→29.92 Å
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Refine LS restraints |
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LS refinement shell |
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