+Open data
-Basic information
Entry | Database: PDB / ID: 7zcl | ||||||
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Title | Unspecific peroxygenase from Collariella virescens | ||||||
Components | (Collariella virescens UPO) x 2 | ||||||
Keywords | OXIDOREDUCTASE / Unspecific peroxygenases (UPO) / Collariella virescens / Short UPO family / Molecular structure / Fatty acid epoxidation | ||||||
Function / homology | HEME C Function and homology information | ||||||
Biological species | Collariella virescens (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Santillana, E. / Romero, A. | ||||||
Funding support | Spain, 1items
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Citation | Journal: Antioxidants / Year: 2022 Title: Structural Characterization of Two Short Unspecific Peroxygenases: Two Different Dimeric Arrangements. Authors: Linde, D. / Santillana, E. / Fernandez-Fueyo, E. / Gonzalez-Benjumea, A. / Carro, J. / Gutierrez, A. / Martinez, A.T. / Romero, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7zcl.cif.gz | 137.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7zcl.ent.gz | 85.3 KB | Display | PDB format |
PDBx/mmJSON format | 7zcl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7zcl_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 7zcl_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 7zcl_validation.xml.gz | 21.4 KB | Display | |
Data in CIF | 7zcl_validation.cif.gz | 30.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zc/7zcl ftp://data.pdbj.org/pub/pdb/validation_reports/zc/7zcl | HTTPS FTP |
-Related structure data
Related structure data | 7zbpC 2yorS 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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Unit cell |
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-Components
#1: Protein | Mass: 25923.533 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Collariella virescens (fungus) / Production host: Escherichia coli (E. coli) / References: unspecific peroxygenase | ||||||
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#2: Protein | Mass: 25994.613 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Collariella virescens (fungus) / Production host: Escherichia coli (E. coli) / References: unspecific peroxygenase | ||||||
#3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.2 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 30% PEG 400, 0.1 M Tris, pH 8.5, 0.2 M sodium citrate |
-Data collection
Diffraction | Mean temperature: 110 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97924 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 4, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97924 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→70.1 Å / Num. obs: 35859 / % possible obs: 100 % / Redundancy: 8.7 % / Biso Wilson estimate: 22.28 Å2 / Rpim(I) all: 0.057 / Rrim(I) all: 0.191 / Net I/σ(I): 10.1 |
Reflection shell | Resolution: 1.95→2.06 Å / Redundancy: 8.4 % / Mean I/σ(I) obs: 2.4 / Num. unique obs: 5682 / Rpim(I) all: 0.4 / Rrim(I) all: 0.99 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2YOR Resolution: 1.95→68.47 Å / SU ML: 0.2163 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.3086 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.54 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→68.47 Å
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Refine LS restraints |
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LS refinement shell |
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