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- PDB-4fh6: Structure of DHP A in complex with 2,4,6-tribromophenol in 10% DMSO -
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Open data
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Basic information
Entry | Database: PDB / ID: 4fh6 | ||||||
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Title | Structure of DHP A in complex with 2,4,6-tribromophenol in 10% DMSO | ||||||
![]() | Dehaloperoxidase A | ||||||
![]() | OXIDOREDUCTASE / peroxidase / globin | ||||||
Function / homology | ![]() oxygen carrier activity / oxygen binding / peroxidase activity / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | de Serrano, V.S. / Franzen, S. | ||||||
![]() | ![]() Title: Structural and Kinetic Study of an Internal Substrate Binding Site in Dehaloperoxidase-Hemoglobin A from Amphitrite ornata. Authors: Zhao, J. / de Serrano, V. / Zhao, J. / Le, P. / Franzen, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 166.6 KB | Display | ![]() |
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PDB format | ![]() | 134.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 19.2 KB | Display | |
Data in CIF | ![]() | 26.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4fh7C ![]() 4ilzC ![]() 2qfkS 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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1 |
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 15548.597 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 6 types, 248 molecules ![](data/chem/img/HEM.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/TBP.gif)
![](data/chem/img/OXY.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/TBP.gif)
![](data/chem/img/OXY.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-DMS / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.79 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.9 Details: 0.2 M Ammonium Sulfate, 32% w/v PEG 4000, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 14, 2010 Details: Rosenbaum-Rock double-crystal monochromator: sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91339 Å / Relative weight: 1 |
Reflection | Resolution: 1.44→35 Å / Num. all: 46777 / Num. obs: 46300 / % possible obs: 98.98 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Biso Wilson estimate: 8.2 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 1.44→1.447 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.413 / Mean I/σ(I) obs: 2.69 / Num. unique all: 3423 / % possible all: 98.61 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2QFK Resolution: 1.44→35 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.928 / SU B: 2.357 / SU ML: 0.041 / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(I): 2 / ESU R: 0.028 / ESU R Free: 0.019 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. The ligand TBP was positioned in the structure by making use of anomalous scattering of bromine atoms to the anomalous difference maps in ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. The ligand TBP was positioned in the structure by making use of anomalous scattering of bromine atoms to the anomalous difference maps in order to locate and position bromine atoms of the tribromophenol molecule
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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 mean: 8.181 Å2
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Refinement step | Cycle: LAST / Resolution: 1.44→35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.44→1.477 Å / Total num. of bins used: 20
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