+Open data
-Basic information
Entry | Database: PDB / ID: 5v5q | ||||||
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Title | Dehaloperoxidase B L9I mutant | ||||||
Components | Dehaloperoxidase B | ||||||
Keywords | OXYGEN TRANSPORT / peroxidase / peroxygenase / globin / mutant | ||||||
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: 1.961 Å | ||||||
Authors | Carey, L.M. / Ghiladi, R.A. | ||||||
Funding support | United States, 1items
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Citation | Journal: Biochim Biophys Acta Proteins Proteom / Year: 2018 Title: How nature tunes isoenzyme activity in the multifunctional catalytic globin dehaloperoxidase from Amphitrite ornata. Authors: Carey, L.M. / Gavenko, R. / Svistunenko, D.A. / Ghiladi, R.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5v5q.cif.gz | 75.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5v5q.ent.gz | 54.8 KB | Display | PDB format |
PDBx/mmJSON format | 5v5q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5v5q_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 5v5q_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 5v5q_validation.xml.gz | 14.8 KB | Display | |
Data in CIF | 5v5q_validation.cif.gz | 19.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v5/5v5q ftp://data.pdbj.org/pub/pdb/validation_reports/v5/5v5q | HTTPS FTP |
-Related structure data
Related structure data | 5v5jC 5v5rC 3ixfS 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 15414.462 Da / Num. of mol.: 2 / Mutation: L9I Source method: isolated from a genetically manipulated source Source: (gene. exp.) Amphitrite ornata (invertebrata) / Plasmid: pET28a Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: Q9NAV7 |
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-Non-polymers , 5 types, 144 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-GOL / | #6: 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: 41.39 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.4 / Details: PEG4000, ammonium sulfate, cacodylate buffer |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 23, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.96→50 Å / Num. obs: 19829 / % possible obs: 99.9 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 15.5 |
Reflection shell | Resolution: 1.96→2.01 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.517 / Num. unique obs: 976 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3IXF Resolution: 1.961→47.805 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.52
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.961→47.805 Å
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Refine LS restraints |
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LS refinement shell |
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