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Yorodumi- PDB-3ok5: Structure of the H55D mutant of dehaloperoxidase-hemoglobin A fro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ok5 | ||||||
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Title | Structure of the H55D mutant of dehaloperoxidase-hemoglobin A from Amphitriti ornata with 4-Bromophenol inhibitor | ||||||
Components | Dehaloperoxidase A | ||||||
Keywords | OXIDOREDUCTASE / globin / peroxidase / dehaloperoxidase | ||||||
Function / homology | Function and homology information oxygen carrier activity / oxygen binding / peroxidase activity / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | Amphitrite ornata (invertebrata) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å | ||||||
Authors | Zhao, J. / De Serrano, V.S. / Franzen, S. | ||||||
Citation | Journal: To be Published Title: Effect of the H55D mutation on the kinetics and structure of dehaloperoxidase-hemoglobin A Authors: Zhao, J. / De Serrano, V.S. / Franzen, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ok5.cif.gz | 86.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ok5.ent.gz | 65.7 KB | Display | PDB format |
PDBx/mmJSON format | 3ok5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ok5_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 3ok5_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 3ok5_validation.xml.gz | 18.2 KB | Display | |
Data in CIF | 3ok5_validation.cif.gz | 26.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ok/3ok5 ftp://data.pdbj.org/pub/pdb/validation_reports/ok/3ok5 | HTTPS FTP |
-Related structure data
Related structure data | 3oj1C 2qfkS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 15525.538 Da / Num. of mol.: 2 / Mutation: H55D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Amphitrite ornata (invertebrata) / Gene: dhpA / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: Q9NAV8 #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.16 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.2M Ammonuim Sulfate, 34% w/v PEG 4000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.91339 Å | |||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 14, 2010 | |||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.91339 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 1.72→48.112 Å / Num. all: 29364 / Num. obs: 27608 / % possible obs: 94.02 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Biso Wilson estimate: 11.24 Å2 / Rmerge(I) obs: 0.139 / Net I/σ(I): 3.38 | |||||||||||||||
Reflection shell | Resolution: 1.72→1.91 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.555 / Mean I/σ(I) obs: 2.38 / Num. unique all: 6936 / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2QFK Resolution: 1.72→35 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.876 / SU B: 3.015 / SU ML: 0.096 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R Free: 0.038 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 11.237 Å2
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Refinement step | Cycle: LAST / Resolution: 1.72→35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.72→1.763 Å / Total num. of bins used: 20
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