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- PDB-6q3d: Dye type peroxidase Aa from Streptomyces lividans: 235.2 kGy structure -
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Open data
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Basic information
Entry | Database: PDB / ID: 6q3d | ||||||
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Title | Dye type peroxidase Aa from Streptomyces lividans: 235.2 kGy structure | ||||||
![]() | Deferrochelatase/peroxidase | ||||||
![]() | OXIDOREDUCTASE / Dye type peroxidase / dose series / serial crystallography / heme | ||||||
Function / homology | ![]() iron import into cell / ferrochelatase activity / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / peroxidase activity / heme binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ebrahim, A. / Moreno-Chicano, T. / Worrall, J.A.R. / Strange, R.W. / Axford, D. / Sherrell, D.A. / Appleby, M. / Owen, R.L. | ||||||
![]() | ![]() Title: Dose-resolved serial synchrotron and XFEL structures of radiation-sensitive metalloproteins. Authors: Ebrahim, A. / Moreno-Chicano, T. / Appleby, M.V. / Chaplin, A.K. / Beale, J.H. / Sherrell, D.A. / Duyvesteyn, H.M.E. / Owada, S. / Tono, K. / Sugimoto, H. / Strange, R.W. / Worrall, J.A.R. / ...Authors: Ebrahim, A. / Moreno-Chicano, T. / Appleby, M.V. / Chaplin, A.K. / Beale, J.H. / Sherrell, D.A. / Duyvesteyn, H.M.E. / Owada, S. / Tono, K. / Sugimoto, H. / Strange, R.W. / Worrall, J.A.R. / Axford, D. / Owen, R.L. / Hough, M.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 | ![]() | 160 KB | Display | ![]() |
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PDB format | ![]() | 124.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 30.6 KB | Display | |
Data in CIF | ![]() | 43.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6i43C ![]() 6i7zC ![]() 6i8eC ![]() 6i8iC ![]() 6i8jC ![]() 6i8kC ![]() 6i8oC ![]() 6i8pC ![]() 6i8qC ![]() 6ibnC ![]() 6q31C ![]() 6q34C ![]() 6q3eC C: citing same article ( |
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Similar structure data |
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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: 39272.016 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: SCO2276 / Production host: ![]() ![]() References: UniProt: Q9RKQ2, Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.16 % / Description: Microcrystals |
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Crystal grow | Temperature: 293 K / Method: batch mode / pH: 8 Details: 7 mg/ml protein mixed with 17% PEG 1500 and 67 mM MIB buffer (comprising imidazole, malonate and boric acid) |
-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: Y |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 28, 2017 |
Radiation | Monochromator: Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 |
Reflection | Resolution: 1.93→44.7 Å / Num. obs: 54263 / % possible obs: 100 % / Redundancy: 46.5 % / CC1/2: 0.966 / R split: 0.172 / Rmerge(I) obs: 0.806 / Net I/σ(I): 2.28 |
Reflection shell | Resolution: 1.93→1.96 Å / Redundancy: 12.7 % / Rmerge(I) obs: 0.874 / Mean I/σ(I) obs: 0.47 / CC1/2: 0.544 / R split: 0.791 / % possible all: 99.8 |
Serial crystallography measurement | Collection time total: 0.25 hours / Collimation: 2x Kirkpatrick-Baez mirror pairs |
Serial crystallography sample delivery | Description: Silicon nitride chips / Method: fixed target |
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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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 91.11 Å2 / Biso mean: 31.8232 Å2 / Biso min: 11.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.93→37.385 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %
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