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- PDB-6d0g: 1.78 Angstrom Resolution Crystal Structure of Quercetin 2,3-dioxy... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6d0g | ||||||
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Title | 1.78 Angstrom Resolution Crystal Structure of Quercetin 2,3-dioxygenase from Acinetobacter baumannii | ||||||
![]() | Pirin family protein | ||||||
![]() | OXIDOREDUCTASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / Quercetin 2 / 3-dioxygenase | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Minasov, G. / Shuvalova, L. / Brunzelle, J.S. / Dubrovska, I. / Kiryukhina, O. / Endres, M. / Anderson, W.F. / Satchell, K.J.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
![]() | ![]() Title: 1.78 Angstrom Resolution Crystal Structure of Quercetin 2,3-dioxygenase from Acinetobacter baumannii. Authors: Minasov, G. / Shuvalova, L. / Brunzelle, J.S. / Dubrovska, I. / Kiryukhina, O. / Endres, M. / Anderson, W.F. / Satchell, K.J.F. / Joachimiak, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 139.3 KB | Display | ![]() |
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PDB format | ![]() | 114.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 425.3 KB | Display | ![]() |
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Full document | ![]() | 426.6 KB | Display | |
Data in XML | ![]() | 15.1 KB | Display | |
Data in CIF | ![]() | 22.1 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 on special symmetry positions |
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Components
#1: Protein | Mass: 36159.066 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: yhhW_2, yhhW_1, A388_00159, A7A65_05705, A7M90_08420, A7N09_08935, AZE33_00735, B4R90_09220, B9X91_00175, BGC29_04645, CAS83_08120, CBE85_14535, CEJ63_12860, CHQ89_16690, CPI82_15400, CV954_18565, LV38_01393 Plasmid: pMCSG68 / Production host: ![]() ![]() | ||
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#2: Chemical | ChemComp-MN / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.7 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 8.0 mg/mL protein in 0.01 M Tris, pH 8.3, screen: PACT (F2) (0.2 M sodium bromide, 0.1 M Bis-Tris propane, pH 6.5, 20% w/v PEG3350) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Feb 6, 2018 / Details: C(111) |
Radiation | Monochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 1.78→30 Å / Num. obs: 29760 / % possible obs: 97.2 % / Observed criterion σ(I): -3 / Redundancy: 13.3 % / Biso Wilson estimate: 24.3 Å2 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.026 / Rrim(I) all: 0.098 / Rsym value: 0.095 / Χ2: 1.382 / Net I/σ(I): 29.3 |
Reflection shell | Resolution: 1.78→1.81 Å / Redundancy: 11.7 % / Rmerge(I) obs: 0.755 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 1272 / CC1/2: 0.773 / Rpim(I) all: 0.223 / Rrim(I) all: 0.79 / Rsym value: 0.755 / Χ2: 0.998 / % possible all: 85.4 |
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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: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.645 Å2
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Refinement step | Cycle: 1 / Resolution: 1.78→29.78 Å
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Refine LS restraints |
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