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- PDB-8iq8: Crystal structure of 3,4-dihydroxyphenylacetate 2,3-dioxygenase (... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8iq8 | ||||||
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Title | Crystal structure of 3,4-dihydroxyphenylacetate 2,3-dioxygenase (DHPAO) from Acinetobacter baumannii | ||||||
![]() | 3,4-dihydroxyphenylacetate 2,3-dioxygenase | ||||||
![]() | OXIDOREDUCTASE / extradiol dioxygenase | ||||||
Function / homology | 3,4-dihydroxyphenylacetate 2,3-dioxygenase / 3,4-dihydroxyphenylacetate 2,3-dioxygenase activity / 3,4-dihydroxyphenylacetate 2,3-dioxygenase / Extradiol ring-cleavage dioxygenase, class III enzyme, subunit B / Catalytic LigB subunit of aromatic ring-opening dioxygenase / : / ferrous iron binding / 3,4-dihydroxyphenylacetate 2,3-dioxygenase![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Chitnumsub, P. / Maenpuen, S. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structure and biochemical characterization of an extradiol 3,4-dihydroxyphenylacetate 2,3-dioxygenase from Acinetobacter baumannii. Authors: Pimviriyakul, P. / Buttranon, S. / Soithongcharoen, S. / Supawatkon, C. / Disayabootr, K. / Watthaisong, P. / Tinikul, R. / Jaruwat, A. / Chaiyen, P. / Chitnumsub, P. / Maenpuen, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 249.1 KB | Display | ![]() |
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PDB format | ![]() | 198.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 452.4 KB | Display | ![]() |
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Full document | ![]() | 458.1 KB | Display | |
Data in XML | ![]() | 48.4 KB | Display | |
Data in CIF | ![]() | 71.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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: 32381.719 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-NA / #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.08 Å3/Da / Density % sol: 60.08 % |
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Crystal grow | Temperature: 298 K / Method: microbatch / pH: 4 Details: 0.1 M PCB buffer pH4 and 25% w/v PEG1500 (Hampton Research kit) PH range: 4-5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() |
Detector | Type: BRUKER PHOTON 100 / Detector: CMOS / Date: Aug 4, 2017 |
Radiation | Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.77→21.03 Å / Num. obs: 147453 / % possible obs: 97.7 % / Redundancy: 4.5 % / CC1/2: 0.993 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.047 / Rrim(I) all: 0.109 / Χ2: 0.99 / Net I/σ(I): 11.4 / Num. measured all: 667103 |
Reflection shell | Resolution: 1.77→1.81 Å / % possible obs: 78.5 % / Redundancy: 1.7 % / Rmerge(I) obs: 0.169 / Num. measured all: 9963 / Num. unique obs: 5851 / CC1/2: 0.92 / Rpim(I) all: 0.149 / Rrim(I) all: 0.226 / Χ2: 1.11 / Net I/σ(I) obs: 5 |
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 8.843 Å2
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Refinement step | Cycle: 1 / Resolution: 1.8→21.04 Å
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Refine LS restraints |
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