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- PDB-2q9o: Near-atomic resolution structure of a Melanocarpus albomyces laccase -
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Open data
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Basic information
Entry | Database: PDB / ID: 2q9o | |||||||||
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Title | Near-atomic resolution structure of a Melanocarpus albomyces laccase | |||||||||
![]() | Laccase-1 | |||||||||
![]() | OXIDOREDUCTASE / laccase / multicopper oxidase / Melanocarpus albomyces / 2-oxohistidine | |||||||||
Function / homology | ![]() extraorganismal space / lignin catabolic process / hydroquinone:oxygen oxidoreductase activity / laccase / cellulose catabolic process / copper ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Hakulinen, N. / Rouvinen, J. | |||||||||
![]() | ![]() Title: A near atomic resolution structure of a Melanocarpus albomyces laccase. Authors: Hakulinen, N. / Andberg, M. / Kallio, J. / Koivula, A. / Kruus, K. / Rouvinen, J. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 514.9 KB | Display | ![]() |
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PDB format | ![]() | 427.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 61858.418 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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-Sugars , 4 types, 15 molecules ![](data/chem/img/NAG.gif)
#2: 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 #3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Polysaccharide | Source method: isolated from a genetically manipulated source #5: Sugar | ChemComp-NAG / |
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-Non-polymers , 6 types, 1462 molecules ![](data/chem/img/CU.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/OXY.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/OXY.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#6: Chemical | ChemComp-CU / #7: Chemical | #8: Chemical | ChemComp-SO4 / #9: Chemical | #10: Chemical | #11: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.24 % |
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Crystal grow | Temperature: 295 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 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.931 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→20 Å / Num. all: 321397 / Num. obs: 310642 / % possible obs: 96.7 % / Rsym value: 0.078 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 1.3→1.4 Å / Mean I/σ(I) obs: 3 / Rsym value: 0.419 / % possible all: 91.5 |
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Processing
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Refinement | Method to determine structure: AB INITIO / Resolution: 1.3→15 Å / Num. parameters: 97288 / Num. restraintsaints: 825301 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ?
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Displacement parameters | Biso mean: 13.989 Å2 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 31 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 10679.65 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.3→15 Å
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Refine LS restraints |
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