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Yorodumi- PDB-6i43: SFX Structure of Damage Free Ferric State of Dye Type Peroxidase ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6i43 | ||||||
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Title | SFX Structure of Damage Free Ferric State of Dye Type Peroxidase Aa from Streptomyces lividans | ||||||
Components | Deferrochelatase/peroxidase | ||||||
Keywords | OXIDOREDUCTASE / peroxidase | ||||||
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 / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.88 Å | ||||||
Authors | Ebrahim, A. / Moreno-Chicano, T. / Chaplin, A.K. / Sherrell, D.A. / Duyvesteyn, H.M.E. / Owada, S. / Tono, K. / Sugimoto, H. / Strange, R.W. / Worrall, J.A.R. | ||||||
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 | 6i43.cif.gz | 159.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6i43.ent.gz | 122.7 KB | Display | PDB format |
PDBx/mmJSON format | 6i43.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i4/6i43 ftp://data.pdbj.org/pub/pdb/validation_reports/i4/6i43 | HTTPS FTP |
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-Related structure data
Related structure data | 6i7zC 6i8eC 6i8iC 6i8jC 6i8kC 6i8oC 6i8pC 6i8qC 6ibnC 6q31C 6q34C 6q3dC 6q3eC 5mapS 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: 40256.020 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: ...Details: DPAGADAGSAVPFHGAHQAGIATPVQDRLHFAAFDVTTEDRAAFVALLKEWTAAARRLTAGHAVGEGAYGGLPEAPPDDTGEALGLKPSRLTLTIGFGPSLFTRFGLADLRPEALADLPKFPGDNLDRARSGGDLCVQACADDPQVAVHAIRNLARIGFGKVVVRWSQLGFGKTSSTTPDKQTPRNLLGFKDGTRNIAGTEKDRLDRFVWAAEKDGTPWMTGGSYLVARRIRMHIETWDRASLQEQEDVFGRDKGEGAPVGKAKERDEPFLKAMKPDAHVRLAHPDSNGGATLLRRGYSFTDGTDGLGRLDAGLFFLAYQRDIRTGFVPVQRNLATDALNEYIQHVGSAVFAVPPGVRDADDWWGSTLFGKEA Source: (gene. exp.) Streptomyces coelicolor A3(2) (bacteria) Gene: SCO2276 / Production host: Escherichia coli BL21(DE3) (bacteria) 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: 2.27 Å3/Da / Density % sol: 45.79 % / Description: Microcrystals |
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Crystal grow | Temperature: 291 K / Method: batch mode / pH: 7 Details: 1:1 ratio of a 6.5 mg/ml DtpAa protein solution with a precipitant solution containing 20% PEG 6000, 100 mM HEPES pH 7.0 |
-Data collection
Diffraction | Mean temperature: 301 K / Serial crystal experiment: Y |
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Diffraction source | Source: FREE ELECTRON LASER / Site: SACLA / Beamline: BL2 / Wavelength: 1.24 Å |
Detector | Type: MPCCD / Detector: CCD / Date: Oct 11, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.24 Å / Relative weight: 1 |
Reflection | Resolution: 1.88→41.46 Å / Num. obs: 57351 / % possible obs: 100 % / Redundancy: 381 % / CC1/2: 0.993 / R split: 0.0722 / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 1.88→1.91 Å / Redundancy: 212 % / Mean I/σ(I) obs: 1.73 / CC1/2: 0.722 / R split: 0.583 / % possible all: 100 |
Serial crystallography measurement | Collection time total: 240 hours / Focal spot size: 1.66 µm2 / Pulse duration: 10 fsec. / Pulse energy: 289 µJ / Pulse photon energy: 10.01 keV / XFEL pulse repetition rate: 30 Hz |
Serial crystallography sample delivery | Description: Silicon nitride fixed target / Method: fixed target |
Serial crystallography sample delivery fixed target | Sample dehydration prevention: Mylar film / Sample solvent: Mother liquor |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB 5MAP Resolution: 1.88→35.458 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 16.03 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.88→35.458 Å
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Refine LS restraints |
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LS refinement shell |
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