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Open data
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Basic information
Entry | Database: PDB / ID: 2d40 | ||||||
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Title | Crystal Structure of Z3393 from Escherichia coli O157:H7 | ||||||
![]() | putative gentisate 1,2-dioxygenase | ||||||
![]() | OXIDOREDUCTASE / Gentisic Acid / 1 / 2-dioxygenase / bicupin / tetramer / Montreal-Kingston Bacterial Structural Genomics Initiative / BSGI / Structural Genomics | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Adams, M.A. / Jia, Z. / Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI) | ||||||
![]() | ![]() Title: Structural and biochemical characterization of gentisate 1,2-dioxygenase from Escherichia coli O157:H7 Authors: Adams, M.A. / Singh, V.K. / Keller, B.O. / Jia, Z. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 250.7 KB | Display | ![]() |
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PDB format | ![]() | 205.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 481.8 KB | Display | ![]() |
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Full document | ![]() | 597.5 KB | Display | |
Data in XML | ![]() | 62.3 KB | Display | |
Data in CIF | ![]() | 84 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
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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: 40229.637 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #2: Chemical | ChemComp-FE / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.9 Å3/Da / Density % sol: 36.4 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 5.9 Details: 0.1M bisTris, 24% PEG 3350, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 297K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 15, 2005 |
Radiation | Monochromator: single crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→34.5 Å / Num. all: 44440 / Num. obs: 43818 / % possible obs: 98 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.5 % / Rmerge(I) obs: 0.073 / Rsym value: 0.063 / Net I/σ(I): 32 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.234 / Mean I/σ(I) obs: 8 / % possible all: 98 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.271 Å2
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Refinement step | Cycle: LAST / Resolution: 2.41→34.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.405→2.467 Å / Total num. of bins used: 20 /
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