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Yorodumi- PDB-4dwu: Carbonmonoxy dehaloperoxidase-hemoglobin A structure at 1.44 Angs... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4dwu | ||||||
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Title | Carbonmonoxy dehaloperoxidase-hemoglobin A structure at 1.44 Angstrom resolution | ||||||
Components | Dehaloperoxidase A | ||||||
Keywords | OXIDOREDUCTASE / peroxidase / globin / hydrogen peroxide / 2 / 4 / 6-trihalophenol | ||||||
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: 1.44 Å | ||||||
Authors | de Serrano, V.S. / Zhao, J. / Franzen, S. | ||||||
Citation | Journal: To be Published 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4dwu.cif.gz | 92.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4dwu.ent.gz | 72.9 KB | Display | PDB format |
PDBx/mmJSON format | 4dwu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4dwu_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 4dwu_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 4dwu_validation.xml.gz | 17.9 KB | Display | |
Data in CIF | 4dwu_validation.cif.gz | 25.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dw/4dwu ftp://data.pdbj.org/pub/pdb/validation_reports/dw/4dwu | HTTPS FTP |
-Related structure data
Related structure data | 4dwtC 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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1 |
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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.) Amphitrite ornata (invertebrata) / Gene: dhpA / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: Q9NAV8, EC: 1.11.-.- #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: 2.15 Å3/Da / Density % sol: 42.88 % |
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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: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.91339 Å | |||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 14, 2010 / Details: Rosenbaum-Rock vertical focusing mirror | |||||||||||||||
Radiation | Monochromator: Rosenbaum-Rock double crystal Si(220) / 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: 1.44→44.2 Å / Num. all: 46314 / Num. obs: 43419 / % possible obs: 93.75 % / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Biso Wilson estimate: 13.8 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 24.6 | |||||||||||||||
Reflection shell | Resolution: 1.44→1.482 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.397 / Mean I/σ(I) obs: 3.2 / Num. unique all: 3356 / % possible all: 57.53 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2QFK Resolution: 1.44→44.2 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.54 / SU ML: 0.056 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(I): 2 / ESU R: 0.019 / ESU R Free: 0.018 / 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 mean: 11.981 Å2
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Refinement step | Cycle: LAST / Resolution: 1.44→44.2 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.44→1.482 Å / Total num. of bins used: 20
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