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- PDB-3ord: Structural Evidence for Stabilization of Inhibitor Binding by a P... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3ord | ||||||
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Title | Structural Evidence for Stabilization of Inhibitor Binding by a Protein Cavity in the Dehaloperoxidase-Hemoglobin from Amphitrite ornata | ||||||
![]() | Dehaloperoxidase A | ||||||
![]() | OXIDOREDUCTASE / globin / peroxidase | ||||||
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 evidence for stabilization of inhibitor binding by a protein cavity in the dehaloperoxidase-hemoglobin from Amphitrite ornata. Authors: de Serrano, V. / 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 | ![]() | 79 KB | Display | ![]() |
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PDB format | ![]() | 60.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 16.2 KB | Display | |
Data in CIF | ![]() | 21.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2qfkS 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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Unit cell |
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Details | monomer |
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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 | ChemComp-XE / #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.7 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.9 Details: 0.2 M ammonium sulfate, 32% 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: RIGAKU SATURN 92 / Detector: CCD / Date: Jul 31, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.22→48.121 Å / Num. all: 13324 / Num. obs: 12423 / % possible obs: 93.24 % / Observed criterion σ(I): 2 / Redundancy: 10.7 % / Biso Wilson estimate: 22.8 Å2 / Rmerge(I) obs: 0.132 / Net I/σ(I): 16.8 |
Reflection shell | Resolution: 2.22→2.278 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.571 / Mean I/σ(I) obs: 3.3 / Num. unique all: 974 / % possible all: 83.61 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2qfk Resolution: 2.22→30.5 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.871 / SU B: 8.192 / SU ML: 0.209 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(I): 2 / ESU R Free: 0.312 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.841 Å2
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Refinement step | Cycle: LAST / Resolution: 2.22→30.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.22→2.278 Å / Total num. of bins used: 20
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