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- PDB-4ilz: Structural and kinetic study of an internal substrate binding sit... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4ilz | ||||||
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Title | Structural and kinetic study of an internal substrate binding site of dehaloperoxidase-hemoglobin A from Amphitrite ornata | ||||||
![]() | 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. / Zhao, J. / Zhao, J. / 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 | ![]() | 88.4 KB | Display | ![]() |
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PDB format | ![]() | 68.6 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 | ![]() | 18.7 KB | Display | |
Data in CIF | ![]() | 25.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4fh6C ![]() 4fh7C ![]() 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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2 | ![]()
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3 | ![]()
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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, 201 molecules ![](data/chem/img/HEM.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/IPA.gif)
![](data/chem/img/TBP.gif)
![](data/chem/img/OXY.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/IPA.gif)
![](data/chem/img/TBP.gif)
![](data/chem/img/OXY.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-IPA / #5: Chemical | ChemComp-TBP / | #6: Chemical | ChemComp-OXY / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.61 % |
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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: liquid nitrogen cooled; sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror |
Radiation | Monochromator: double crystal - liquid nitrogen cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91339 Å / Relative weight: 1 |
Reflection | Resolution: 1.91→48 Å / Num. all: 20247 / Num. obs: 20174 / % possible obs: 99.64 % / Observed criterion σ(I): 2 / Biso Wilson estimate: 8.3 Å2 / Rmerge(I) obs: 0.156 / Net I/σ(I): 2.18 |
Reflection shell | Resolution: 1.91→1.959 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.313 / Mean I/σ(I) obs: 4.2 / Num. unique all: 1470 / % possible all: 99.29 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 2QFK Resolution: 1.91→48 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.859 / SU B: 4.041 / SU ML: 0.122 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(I): 2 / ESU R: 0.065 / ESU R Free: 0.047 / 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: 6.724 Å2
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Refinement step | Cycle: LAST / Resolution: 1.91→48 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.91→1.959 Å / Total num. of bins used: 20
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