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- PDB-4fh7: Structure of DHP A in complex with 2,4,6-tribromophenol in 20% me... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4fh7 | ||||||
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Title | Structure of DHP A in complex with 2,4,6-tribromophenol in 20% methanol | ||||||
![]() | 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 | ![]() | 92.9 KB | Display | ![]() |
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PDB format | ![]() | 72.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 19.6 KB | Display | |
Data in CIF | ![]() | 27.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4fh6C ![]() 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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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, 259 molecules ![](data/chem/img/HEM.gif)
![](data/chem/img/TBP.gif)
![](data/chem/img/OXY.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/MOH.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/TBP.gif)
![](data/chem/img/OXY.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/MOH.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-TBP / | #4: Chemical | ChemComp-OXY / | #5: Chemical | ChemComp-SO4 / #6: Chemical | ChemComp-MOH / #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: 42.7 % |
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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: 1.74→35 Å / Num. all: 26670 / Num. obs: 26593 / % possible obs: 99.71 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 10.7 Å2 / Rmerge(I) obs: 0.116 / Net I/σ(I): 5.1 |
Reflection shell | Resolution: 1.74→1.784 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.428 / Mean I/σ(I) obs: 4 / Num. unique all: 1946 / % possible all: 98.38 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2QFK Resolution: 1.74→35 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.893 / SU B: 2.988 / SU ML: 0.095 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(I): 2 / ESU R: 0.044 / ESU R Free: 0.037 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 9.608 Å2
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Refinement step | Cycle: LAST / Resolution: 1.74→35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.74→1.784 Å / Total num. of bins used: 20
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