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Yorodumi- PDB-6fkt: Crystal structure of a dye-decolorizing peroxidase R232A variant ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6fkt | |||||||||
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Title | Crystal structure of a dye-decolorizing peroxidase R232A variant from Klebsiella pneumoniae (KpDyP) | |||||||||
Components | Iron-dependent peroxidase | |||||||||
Keywords | OXIDOREDUCTASE / alpha-beta barrel / heme binding / DyP / enzymatic redox reaction | |||||||||
Function / homology | Function and homology information Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / peroxidase activity / heme binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Klebsiella pneumoniae (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86002782211 Å | |||||||||
Authors | Pfanzagl, V. / Hofbauer, S. / Mlynek, G. | |||||||||
Funding support | Austria, 2items
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Citation | Journal: J. Biol. Chem. / Year: 2018 Title: Roles of distal aspartate and arginine of B-class dye-decolorizing peroxidase in heterolytic hydrogen peroxide cleavage. Authors: Pfanzagl, V. / Nys, K. / Bellei, M. / Michlits, H. / Mlynek, G. / Battistuzzi, G. / Djinovic-Carugo, K. / Van Doorslaer, S. / Furtmuller, P.G. / Hofbauer, S. / Obinger, C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6fkt.cif.gz | 440.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6fkt.ent.gz | 302.3 KB | Display | PDB format |
PDBx/mmJSON format | 6fkt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fk/6fkt ftp://data.pdbj.org/pub/pdb/validation_reports/fk/6fkt | HTTPS FTP |
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-Related structure data
Related structure data | 6fiyC 6fksSC 6fl2C 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 33367.488 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) Gene: yfeX, AGG09_21550, B1727_13990, B8011_07420, BL102_0001560, BN49_3985, BVX91_12125, CEO55_07245, CIT28_09840, CP905_14695, PMK1_00271, SAMEA3531778_01640, SM57_03027 Variant: R232A Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: A0A0W8ATM9, Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases #2: Chemical | #3: Chemical | ChemComp-MG / | #4: 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: 2.25 Å3/Da / Density % sol: 45.43 % |
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Crystal grow | Temperature: 298.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 29% w/v PEG 3350, 0.15 M MgCl2, 0.1 M Tris-HCl, pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.996 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jun 17, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.996 Å / Relative weight: 1 |
Reflection | Resolution: 1.86→75.23 Å / Num. obs: 51833 / % possible obs: 99.26 % / Redundancy: 6.4 % / Biso Wilson estimate: 27.2494625903 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.1134 / Rpim(I) all: 0.04821 / Rrim(I) all: 0.1235 / Net I/σ(I): 12.11 |
Reflection shell | Resolution: 1.86→1.927 Å / Redundancy: 6.6 % / Rmerge(I) obs: 1.701 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 4908 / CC1/2: 0.589 / Rpim(I) all: 0.7093 / Rrim(I) all: 1.847 / % possible all: 96.57 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6FKS Resolution: 1.86002782211→75.2221720275 Å / SU ML: 0.21672739977 / Cross valid method: FREE R-VALUE / σ(F): 1.32698463845 / Phase error: 21.1932223435
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.6521148601 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.86002782211→75.2221720275 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 11.7947656621 Å / Origin y: 23.8383687836 Å / Origin z: 17.3385096472 Å
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Refinement TLS group | Selection details: all |