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- PDB-7dlk: Crystal Structure of veratryl alcohol bound Dye Decolorizing pero... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7dlk | ||||||
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Title | Crystal Structure of veratryl alcohol bound Dye Decolorizing peroxidase from Bacillus subtilis | ||||||
![]() | Deferrochelatase/peroxidase | ||||||
![]() | OXIDOREDUCTASE / Dye-decolorizing peroxidase / ferredoxin like fold / Veratryl alcohol | ||||||
Function / homology | ![]() iron import into cell / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / peroxidase activity / membrane => GO:0016020 / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Dhankhar, P. / Dalal, V. / Kumar, P. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of dye-decolorizing peroxidase from Bacillus subtilis in complex with veratryl alcohol. Authors: Dhankhar, P. / Dalal, V. / Singh, V. / Sharma, A.K. / Kumar, P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 478.7 KB | Display | ![]() |
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PDB format | ![]() | 389.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 11 MB | Display | ![]() |
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Full document | ![]() | 10.9 MB | Display | |
Data in XML | ![]() | 106.9 KB | Display | |
Data in CIF | ![]() | 150.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6kmmS 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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1 | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 6 molecules ABCDEF
#1: Protein | Mass: 40235.324 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: A0A6G2J275, Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases |
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-Non-polymers , 9 types, 1962 molecules ![](data/chem/img/HEM.gif)
![](data/chem/img/OXY.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/VOH.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/OXY.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/VOH.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-HEM / #3: Chemical | ChemComp-OXY / #4: Chemical | #5: Chemical | ChemComp-GOL / #6: Chemical | ChemComp-CL / #7: Chemical | ChemComp-PO4 / | #8: Chemical | #9: Chemical | ChemComp-EPE / | #10: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.44 Å3/Da / Density % sol: 64.29 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 26% MPD, 0.05 M HEPES |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Nov 19, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9677 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→45.68 Å / Num. obs: 170472 / % possible obs: 90.6 % / Redundancy: 3.38 % / CC1/2: 0.99 / Net I/σ(I): 7.6 |
Reflection shell | Resolution: 2.1→2.2 Å / Num. unique obs: 23937 / CC1/2: 0.82 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6KMM Resolution: 2.1→45.68 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.935 / SU B: 6.509 / SU ML: 0.157 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.194 / ESU R Free: 0.189 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 200.94 Å2 / Biso mean: 49.41 Å2 / Biso min: 20.69 Å2
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Refinement step | Cycle: final / Resolution: 2.1→45.68 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.155 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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