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Yorodumi- PDB-8vzr: Crystal structure of dehaloperoxidase A in complex with substrate... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8vzr | ||||||
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Title | Crystal structure of dehaloperoxidase A in complex with substrate 4-bromo-o-cresol | ||||||
Components | Dehaloperoxidase A | ||||||
Keywords | OXIDOREDUCTASE / peroxidsase / peroxygenase / oxidase / oxygenase / globin / heme cofactor / oxygen binding / hydrogen preoxide cosubstrate / halophenol binding / substrate | ||||||
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: 1.64 Å | ||||||
Authors | Aktar, M.S. / de Serrano, V.S. / Ghiladi, R.A. / Franzen, S. | ||||||
Funding support | United States, 1items
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Citation | Journal: Biochemistry / Year: 2024 Title: Structural Comparison of Substrate Binding Sites in Dehaloperoxidase A and B. Authors: Aktar, M.S. / de Serrano, V. / Ghiladi, R.A. / Franzen, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8vzr.cif.gz | 201 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8vzr.ent.gz | 123.5 KB | Display | PDB format |
PDBx/mmJSON format | 8vzr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8vzr_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 8vzr_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 8vzr_validation.xml.gz | 19.2 KB | Display | |
Data in CIF | 8vzr_validation.cif.gz | 25.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vz/8vzr ftp://data.pdbj.org/pub/pdb/validation_reports/vz/8vzr | HTTPS FTP |
-Related structure data
Related structure data | 8vkcC 8vkdC 8vskC 2qfkS 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: 15548.597 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: Q9NAV8 |
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-Non-polymers , 8 types, 196 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-GOL / #5: Chemical | #6: Chemical | ChemComp-PG4 / | #7: Chemical | #8: Chemical | #9: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 2.17 Å3/Da / Density % sol: 43.28 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / Details: MPEG2000, ammonium sulfate, sodium cacodylate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Nov 3, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.64→37.14 Å / Num. obs: 33787 / % possible obs: 99.79 % / Redundancy: 9.3 % / CC1/2: 0.987 / Net I/σ(I): 30.8 |
Reflection shell | Resolution: 1.64→1.682 Å / Num. unique obs: 2361 / CC1/2: 0.712 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2QFK Resolution: 1.64→37.136 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.939 / SU B: 4.841 / SU ML: 0.073 / Cross valid method: FREE R-VALUE / ESU R: 0.191 / ESU R Free: 0.104 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: 19.16 Å2
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Refinement step | Cycle: LAST / Resolution: 1.64→37.136 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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