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Yorodumi- PDB-9f1t: Psychrophilic laccase (multicopper oxidase) from Oenococcus oeni ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 9f1t | ||||||||||||
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Title | Psychrophilic laccase (multicopper oxidase) from Oenococcus oeni 229 without Histag | ||||||||||||
Components | Multicopper oxidase | ||||||||||||
Keywords | OXIDOREDUCTASE / Laccase / oxidorreductase / multicopper oxidase | ||||||||||||
Function / homology | Function and homology information | ||||||||||||
Biological species | Oenococcus oeni (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||||||||
Authors | Paredes, F. / Casino, P. | ||||||||||||
Funding support | Spain, 3items
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Citation | Journal: Int J Mol Sci / Year: 2024 Title: Biochemical and Structural Characterization of a Novel Psychrophilic Laccase (Multicopper Oxidase) Discovered from Oenococcus oeni 229 (ENOLAB 4002). Authors: Olmeda, I. / Paredes, F. / Sendra, R. / Casino, P. / Pardo, I. / Ferrer, S. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9f1t.cif.gz | 194.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9f1t.ent.gz | 153.5 KB | Display | PDB format |
PDBx/mmJSON format | 9f1t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9f1t_validation.pdf.gz | 434.6 KB | Display | wwPDB validaton report |
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Full document | 9f1t_full_validation.pdf.gz | 443.8 KB | Display | |
Data in XML | 9f1t_validation.xml.gz | 34.1 KB | Display | |
Data in CIF | 9f1t_validation.cif.gz | 46.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f1/9f1t ftp://data.pdbj.org/pub/pdb/validation_reports/f1/9f1t | HTTPS FTP |
-Related structure data
Related structure data | 9f3zC 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: 55591.949 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oenococcus oeni (bacteria) / Gene: OEOE_0009 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q04HQ8 #2: Chemical | ChemComp-CU / #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.2289659 Å3/Da / Density % sol: 44.84415 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 18% PEG 10000, 20% glycerol, 100 mM Tris-HCl pH 8.5 and 100 mM NaCl |
-Data collection
Diffraction | Mean temperature: 180 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 29, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97926 Å / Relative weight: 1 |
Reflection | Resolution: 3→68.65 Å / Num. obs: 19139 / % possible obs: 97.8 % / Redundancy: 4.7 % / CC1/2: 0.912 / Rmerge(I) obs: 0.299 / Rpim(I) all: 0.15 / Rrim(I) all: 0.336 / Χ2: 0.85 / Net I/σ(I): 4.4 |
Reflection shell | Resolution: 3→3.18 Å / % possible obs: 97.8 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.788 / Num. measured all: 14384 / Num. unique obs: 3066 / CC1/2: 0.66 / Rpim(I) all: 0.401 / Rrim(I) all: 0.889 / Χ2: 0.92 / Net I/σ(I) obs: 2.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→68.65 Å / Cor.coef. Fo:Fc: 0.892 / Cor.coef. Fo:Fc free: 0.831 / SU B: 27.52 / SU ML: 0.487 / Cross valid method: THROUGHOUT / ESU R Free: 0.524 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.207 Å2
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Refinement step | Cycle: 1 / Resolution: 3→68.65 Å
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