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- PDB-4dwt: Carbonmonoxy dehaloperoxidase-hemoglobin A structure at 2.05 Angs... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4dwt | ||||||
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Title | Carbonmonoxy dehaloperoxidase-hemoglobin A structure at 2.05 Angstrom resolution | ||||||
![]() | Dehaloperoxidase A | ||||||
![]() | OXIDOREDUCTASE / peroxidase / globin / hydrogen peroxide / 2 / 4 / 6-trihalophenol | ||||||
Function / homology | ![]() oxygen carrier activity / oxygen binding / peroxidase activity / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | de Serrano, V.S. / Zhao, J. / Franzen, S. | ||||||
![]() | ![]() Title: A unique role for the distal histidine observed in carbonmonoxy dehaloperoxidase-hemoglobin A structures Authors: de Serrano, V.S. / Zhao, J. / 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 | ![]() | 91.5 KB | Display | ![]() |
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PDB format | ![]() | 72.2 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 | ![]() | 18.2 KB | Display | |
Data in CIF | ![]() | 25.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4dwuC ![]() 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
#1: Protein | Mass: 15548.597 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.02 % |
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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 PEG4000, 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: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 22, 2010 / Details: Osmic Confocal X-ray optics |
Radiation | Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→35 Å / Num. all: 16589 / Num. obs: 16541 / % possible obs: 99.71 % / Observed criterion σ(I): 2 / Redundancy: 4.8 % / Biso Wilson estimate: 21.4 Å2 / Rmerge(I) obs: 0.131 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 2.05→2.102 Å / Redundancy: 5 % / Rmerge(I) obs: 0.666 / Mean I/σ(I) obs: 2.3 / Num. unique all: 1171 / % possible all: 98.71 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2QFK Resolution: 2.05→35 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.919 / SU B: 4.687 / SU ML: 0.124 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.047 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT 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 mean: 19.536 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.102 Å / Total num. of bins used: 20
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