[English] 日本語
Yorodumi- PDB-8vkc: Crystal structure of dehaloperoxidase A in complex with substrate... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8vkc | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of dehaloperoxidase A in complex with substrate 4-nitrophenol | ||||||
Components | Dehaloperoxidase A | ||||||
Keywords | OXIDOREDUCTASE / peroxidase / peroxigenase / oxidase / oxigenase / globin / heme cofactor / oxigen binding / hydrogen peroxide co-substrate / halphenol substrates | ||||||
Function / homology | Function and homology information oxygen carrier activity / peroxidase activity / oxygen binding / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | Amphitrite ornata (invertebrata) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å | ||||||
Authors | Aktar, M.S. / de Serrano, V.S. / Ghiladi, R.A. / Franzen, S. | ||||||
Funding support | United States, 1items
| ||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8vkc.cif.gz | 134.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8vkc.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8vkc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8vkc_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8vkc_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 8vkc_validation.xml.gz | 15.3 KB | Display | |
Data in CIF | 8vkc_validation.cif.gz | 20.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vk/8vkc ftp://data.pdbj.org/pub/pdb/validation_reports/vk/8vkc | HTTPS FTP |
-Related structure data
Related structure data | 8vkdC 8vskC 8vzrC 2qfkS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 2 molecules AAABBB
#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 |
---|
-Non-polymers , 5 types, 111 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-GOL / | #5: Chemical | #6: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.93 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / Details: MPEG 2000, ammonium sulfate, sodium cacodylate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Sep 25, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.03→30.43 Å / Num. obs: 16983 / % possible obs: 93.05 % / Redundancy: 3.7 % / CC1/2: 0.98 / Net I/σ(I): 12.4 |
Reflection shell | Resolution: 2.03→2.083 Å / Num. unique obs: 973 / CC1/2: 0.314 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2QFK Resolution: 2.03→30.43 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.901 / SU B: 15.382 / SU ML: 0.183 / Cross valid method: FREE R-VALUE / ESU R Free: 0.233 Details: Hydrogens have been added in their riding positions
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 28.825 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.03→30.43 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|