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- PDB-6d0p: 1.88 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: 6d0p | ||||||
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Title | 1.88 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: 1.88 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 | ![]() | 500.8 KB | Display | ![]() |
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PDB format | ![]() | 430.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 497.1 KB | Display | ![]() |
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Full document | ![]() | 506.3 KB | Display | |
Data in XML | ![]() | 55.4 KB | Display | |
Data in CIF | ![]() | 81.4 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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1 | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 32480.059 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: A7N09_17085, B4R90_18685, B9X95_09530, BGC29_11425, BWP00_02730, CPI82_04080, CV950_06630, CV954_00950, IX87_13390 Plasmid: pMCSG73 / Production host: ![]() ![]() |
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-Non-polymers , 9 types, 1075 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-MN / #4: Chemical | ChemComp-PEG / #5: Chemical | #6: Chemical | #7: Chemical | ChemComp-EDO / | #8: Chemical | #9: Chemical | ChemComp-PGE / | #10: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.86 Å3/Da / Density % sol: 57 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 8.5 mg/mL protein in 0.01 M Tris, pH 8.3, screen: Classics II (H1) (0.2 M ammonium acetate, 0.1 M Bis-Tris, pH 8.5, 25% 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: Mar 14, 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: 1.88→30 Å / Num. obs: 120737 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Biso Wilson estimate: 24.4 Å2 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.05 / Rrim(I) all: 0.107 / Rsym value: 0.094 / Χ2: 1.216 / Net I/σ(I): 15.7 |
Reflection shell | Resolution: 1.88→1.91 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.763 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 6014 / CC1/2: 0.649 / Rpim(I) all: 0.404 / Rrim(I) all: 0.865 / Rsym value: 0.763 / Χ2: 1.004 / % possible all: 100 |
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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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.715 Å2
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Refinement step | Cycle: 1 / Resolution: 1.88→29.81 Å
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Refine LS restraints |
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