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- PDB-6fks: Crystal structure of a dye-decolorizing peroxidase from Klebsiell... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6fks | |||||||||
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Title | Crystal structure of a dye-decolorizing peroxidase from Klebsiella pneumoniae (KpDyP) | |||||||||
![]() | Iron-dependent peroxidase | |||||||||
![]() | OXIDOREDUCTASE / alpha-beta barrel / heme binding / DyP / enzymatic redox reaction | |||||||||
Function / homology | ![]() Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / peroxidase activity / heme binding / metal ion binding / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Pfanzagl, V. / Hofbauer, S. / Mlynek, G. | |||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 423.9 KB | Display | ![]() |
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PDB format | ![]() | 300.1 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 | ![]() | 28.6 KB | Display | |
Data in CIF | ![]() | 42.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6fiyC ![]() 6fktC ![]() 6fl2C ![]() 5de0S C: citing same article ( S: Starting model for refinement |
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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: 33453.605 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() 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 Production host: ![]() ![]() References: UniProt: A0A0W8ATM9, Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases #2: Chemical | #3: Chemical | ChemComp-GOL / #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.18 % |
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Crystal grow | Temperature: 298.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 23% w/v PEG 3350, 0.1 M MgCl2, 0.1 M Tris-HCl, pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 11, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→52.22 Å / Num. obs: 69426 / % possible obs: 96.86 % / Redundancy: 3.1 % / Biso Wilson estimate: 17.7363405784 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.04149 / Rpim(I) all: 0.02764 / Rrim(I) all: 0.05004 / Net I/σ(I): 16.64 |
Reflection shell | Resolution: 1.6→1.675 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.4457 / Mean I/σ(I) obs: 2.21 / Num. unique obs: 6619 / CC1/2: 0.802 / Rpim(I) all: 0.3253 / Rrim(I) all: 0.5549 / % possible all: 93.09 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5de0 Resolution: 1.60000463928→52.2177435523 Å / SU ML: 0.141380258865 / Cross valid method: FREE R-VALUE / σ(F): 1.34753647333 / Phase error: 16.1468497068
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.7530478625 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.60000463928→52.2177435523 Å
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Refine LS restraints |
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LS refinement shell |
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