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Yorodumi- PDB-3fu7: Melanocarpus albomyces laccase crystal soaked (4 sec) with 2,6-di... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3fu7 | |||||||||
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Title | Melanocarpus albomyces laccase crystal soaked (4 sec) with 2,6-dimethoxyphenol | |||||||||
Components | (Laccase-1) x 2 | |||||||||
Keywords | OXIDOREDUCTASE / Laccase / multicopper oxidase / complex structure / 2 / 6-dimethoxyphenol / oxidation of phenolic compounds / Glycoprotein / Lignin degradation / Metal-binding | |||||||||
Function / homology | Function and homology information extraorganismal space / lignin catabolic process / hydroquinone:oxygen oxidoreductase activity / laccase / cellulose catabolic process / copper ion binding Similarity search - Function | |||||||||
Biological species | Melanocarpus albomyces (fungus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å | |||||||||
Authors | Kallio, J.P. / Hakulinen, N. / Rouvinen, J. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2009 Title: Structure Function Studies of a Melanocarpus albomyces Laccase Suggest a Pathway for Oxidation of Phenolic Compounds. Authors: Kallio, J.P. / Auer, S. / Janis, J. / Andberg, M. / Kruus, K. / Rouvinen, J. / Koivula, A. / Hakulinen, N. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3fu7.cif.gz | 265.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3fu7.ent.gz | 211.1 KB | Display | PDB format |
PDBx/mmJSON format | 3fu7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3fu7_validation.pdf.gz | 3.5 MB | Display | wwPDB validaton report |
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Full document | 3fu7_full_validation.pdf.gz | 3.5 MB | Display | |
Data in XML | 3fu7_validation.xml.gz | 52.5 KB | Display | |
Data in CIF | 3fu7_validation.cif.gz | 78.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fu/3fu7 ftp://data.pdbj.org/pub/pdb/validation_reports/fu/3fu7 | HTTPS FTP |
-Related structure data
Related structure data | 3fu8C 3fu9C 2q9oS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 61858.418 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Melanocarpus albomyces (fungus) / Strain: VTT D-96490 / Gene: LAC1 / Production host: Trichoderma reesei (fungus) / Strain (production host): RUTC-30 / References: UniProt: Q70KY3, laccase |
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#2: Protein | Mass: 61845.441 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Melanocarpus albomyces (fungus) / Strain: VTT D-96490 / Gene: LAC1 / Production host: Trichoderma reesei (fungus) / Strain (production host): RUTC-30 / References: UniProt: Q70KY3, laccase |
-Sugars , 4 types, 14 molecules
#3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #5: Polysaccharide | Source method: isolated from a genetically manipulated source #9: Sugar | ChemComp-NAG / |
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-Non-polymers , 8 types, 971 molecules
#6: Chemical | ChemComp-CU / #7: Chemical | #8: Chemical | #10: Chemical | #11: Chemical | ChemComp-3DM / | #12: Chemical | ChemComp-D2M / | #13: Chemical | ChemComp-KIA / | #14: Water | ChemComp-HOH / | |
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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: 2.71 Å3/Da / Density % sol: 54.56 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 15 % PMME 2000, 0,2 M ammonium sulphate, 0,1 M sodium acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 1.365 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 22, 2006 / Details: mirrors |
Radiation | Monochromator: Double crystal Si[111], horizontally focussing Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.365 Å / Relative weight: 1 |
Reflection | Resolution: 1.67→20 Å / Num. all: 149347 / Num. obs: 149347 / % possible obs: 97.2 % / Redundancy: 3.3 % / Biso Wilson estimate: 22 Å2 / Rsym value: 0.068 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 1.67→1.7 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 4.2 / Num. unique all: 6162 / Rsym value: 0.25 / % possible all: 77.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2q9o Resolution: 1.67→19.61 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.925 / SU B: 1.883 / SU ML: 0.065 / Cross valid method: THROUGHOUT / ESU R: 0.103 / ESU R Free: 0.101 / 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: 17.022 Å2
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Refinement step | Cycle: LAST / Resolution: 1.67→19.61 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.67→1.715 Å / Total num. of bins used: 20
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