+Open data
-Basic information
Entry | Database: PDB / ID: 7t9c | ||||||
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Title | Crystal structure of dehaloperoxidase B in complex with thymol | ||||||
Components | Dehaloperoxidase B | ||||||
Keywords | OXIDOREDUCTASE / dehaloperoxidase B / heme peroxidase / peroxigenase / oxygen binding / heme cofactor | ||||||
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: 1.73 Å | ||||||
Authors | de Serrano, V.S. / Ghiladi, R.A. / Malewschik, T. / Yun, D. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: The Multifunctional Globin Dehaloperoxidase as a Biocatalyst in the Oxidation of Monoterpenes Authors: Malewschik, T. / de Serrano, V.S. / Yun, D. / 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 | 7t9c.cif.gz | 132.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7t9c.ent.gz | 100.5 KB | Display | PDB format |
PDBx/mmJSON format | 7t9c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7t9c_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 7t9c_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 7t9c_validation.xml.gz | 17.8 KB | Display | |
Data in CIF | 7t9c_validation.cif.gz | 23.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t9/7t9c ftp://data.pdbj.org/pub/pdb/validation_reports/t9/7t9c | HTTPS FTP |
-Related structure data
Related structure data | 7sjbC 7sjcC 7sjdC 7sjeC 7sjfC 7sjgC 7sjhC 7sjiC 7t9dC 7t9eC 3ixfS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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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 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Amphitrite ornata (invertebrata) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9NAV7 |
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-Non-polymers , 5 types, 120 molecules
#2: Chemical | #3: Chemical | ChemComp-GOL / #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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Sequence details | LIGAND IPB OCCUPIES DENSITY THAT IS CLOSE TO THE POSITION OF H55 IN ITS ALTERNATE CONFORMATION. THE ...LIGAND IPB OCCUPIES DENSITY THAT IS CLOSE TO THE POSITION OF H55 IN ITS ALTERNATE CONFORMATI |
-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: 42.82 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / Details: MPEG 2000, ammonium sulfate, Na cacodylate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 21, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.73→29.99 Å / Num. obs: 27496 / % possible obs: 96.7 % / Redundancy: 4 % / CC1/2: 0.995 / Net I/σ(I): 20.5 |
Reflection shell | Resolution: 1.73→1.789 Å / Num. unique obs: 1983 / CC1/2: 0.712 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3IXF Resolution: 1.73→29.99 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.954 / SU B: 6.161 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.139 / ESU R Free: 0.119 Details: Hydrogens have been added in their riding positions
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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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.796 Å2
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Refinement step | Cycle: LAST / Resolution: 1.73→29.99 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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