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Yorodumi- PDB-6q3e: Dye type peroxidase Aa from Streptomyces lividans: 274.4 kGy structure -
+Open data
-Basic information
Entry | Database: PDB / ID: 6q3e | ||||||
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Title | Dye type peroxidase Aa from Streptomyces lividans: 274.4 kGy structure | ||||||
Components | Deferrochelatase/peroxidase | ||||||
Keywords | OXIDOREDUCTASE / Dye type peroxidase / dose series / serial crystallography / heme | ||||||
Function / homology | Function and homology information 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 | Streptomyces coelicolor A3 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å | ||||||
Authors | Ebrahim, A. / Moreno-Chicano, T. / Worrall, J.A.R. / Strange, R.W. / Axford, D. / Sherrell, D.A. / Appleby, M. / Owen, R.L. | ||||||
Citation | Journal: Iucrj / Year: 2019 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6q3e.cif.gz | 158.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6q3e.ent.gz | 123.1 KB | Display | PDB format |
PDBx/mmJSON format | 6q3e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q3/6q3e ftp://data.pdbj.org/pub/pdb/validation_reports/q3/6q3e | HTTPS FTP |
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-Related structure data
Related structure data | 6i43SC 6i7zC 6i8eC 6i8iC 6i8jC 6i8kC 6i8oC 6i8pC 6i8qC 6ibnC 6q31C 6q34C 6q3dC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Streptomyces coelicolor A3(2) (bacteria) Gene: SCO2276 / Production host: Escherichia coli (E. coli) 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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 28, 2018 |
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: 2.03→44.7 Å / Num. obs: 46140 / % possible obs: 100 % / Redundancy: 44.5 % / CC1/2: 0.969 / R split: 0.179 / Rmerge(I) obs: 0.765 / Net I/σ(I): 2.02 |
Reflection shell | Resolution: 2.03→2.07 Å / Redundancy: 11.4 % / Rmerge(I) obs: 0.859 / Mean I/σ(I) obs: 0.5 / CC1/2: 0.506 / R split: 0.783 / % possible all: 99.6 |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6I43 Resolution: 2.03→37.386 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.83
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 89.76 Å2 / Biso mean: 32.5936 Å2 / Biso min: 11.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.03→37.386 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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