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- PDB-7mnh: V59W mutant of Dehaloperoxidase A from Amphitrite ornata treated ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7mnh | ||||||
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Title | V59W mutant of Dehaloperoxidase A from Amphitrite ornata treated with Fluoride | ||||||
![]() | Dehaloperoxidase A | ||||||
![]() | OXIDOREDUCTASE / Dehaloperoxidase A / Amphitrite ornata / DHP | ||||||
Function / homology | ![]() oxygen carrier activity / oxygen binding / peroxidase activity / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Shay, M.R. / Thompson, M.K. / Franzen, S. | ||||||
![]() | ![]() Title: A new inhibition mechanism in the multifunctional catalytic hemoglobin dehaloperoxidase as revealed by the DHP A(V59W) mutant: A spectroscopic and crystallographic study Authors: Thompson, M.K. / Shay, M.R. / Dumarieh, R. / Ghiladi, R.A. / 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 | ![]() | 82.2 KB | Display | ![]() |
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PDB format | ![]() | 59.6 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 | ![]() | 17.5 KB | Display | |
Data in CIF | ![]() | 25.5 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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Unit cell |
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Components
#1: Protein | Mass: 15766.873 Da / Num. of mol.: 2 / Mutation: V59W Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.31 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: Protein solution: 8mg/mL protein 20 mM Sodium Cacodylate, pH 6.5 Crystallization: 0.2 M Ammonium Sulfate 30-36% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Oct 1, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.24→48.26 Å / Num. obs: 75146 / % possible obs: 97.5 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 3.34 |
Reflection shell | Resolution: 1.24→1.28 Å / Rmerge(I) obs: 0.55 / Num. unique obs: 7502 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2QFK Resolution: 1.24→48.26 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.957 / SU ML: 0 / SU R Cruickshank DPI: 0.0454 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.043 / ESU R Free: 0.048 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 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 max: 44.6 Å2 / Biso mean: 10.547 Å2 / Biso min: 2.89 Å2
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Refinement step | Cycle: final / Resolution: 1.24→48.26 Å
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LS refinement shell | Resolution: 1.24→1.272 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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