+Open data
-Basic information
Entry | Database: PDB / ID: 4jhu | |||||||||
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Title | T2-depleted laccase from Coriolopsis caperata soaked with CuCl | |||||||||
Components | LACCASE | |||||||||
Keywords | OXIDOREDUCTASE / BETA SHEET / 4-COPPER PROTEIN / METAL-BINDING / LACCASE | |||||||||
Function / homology | Function and homology information hydroquinone:oxygen oxidoreductase activity / laccase / copper ion binding / extracellular region Similarity search - Function | |||||||||
Biological species | Coriolopsis Caperata (fungus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å | |||||||||
Authors | Polyakov, K.M. / Fedorova, T.V. / Glazunova, O.A. / Kurzeev, S.A. / Maloshenok, L.G. / Koroleva, O.A. | |||||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2015 Title: Elucidation of the crystal structure of Coriolopsis caperata laccase: restoration of the structure and activity of the native enzyme from the T2-depleted form by copper ions. Authors: Glazunova, O.A. / Polyakov, K.M. / Fedorova, T.V. / Dorovatovskii, P.V. / Koroleva, O.V. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4jhu.cif.gz | 116 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4jhu.ent.gz | 90.5 KB | Display | PDB format |
PDBx/mmJSON format | 4jhu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jh/4jhu ftp://data.pdbj.org/pub/pdb/validation_reports/jh/4jhu | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 53371.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coriolopsis Caperata (fungus) / References: UniProt: M1GME7*PLUS | ||||||
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#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Chemical | ChemComp-CU / #4: Chemical | ChemComp-PG4 / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.89 Å3/Da / Density % sol: 57.41 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 20% PEG 8000, 0.1 M HEPES, hanging drop, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: KURCHATOV SNC / Beamline: K4.4 / Wavelength: 0.99 Å | |||||||||||||||||||||
Detector | Type: MARRESEARCH / Detector: CCD / Date: Oct 12, 2011 | |||||||||||||||||||||
Radiation | Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 0.99 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 1.89→20 Å / Num. all: 50253 / Num. obs: 49260 / % possible obs: 98.02 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 23.518 Å2 | |||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.89→19.37 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.939 / SU B: 2.685 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.121 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.673 Å2
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Refinement step | Cycle: LAST / Resolution: 1.89→19.37 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.89→1.941 Å / Total num. of bins used: 20
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