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- PDB-2xyb: CRYSTAL STRUCTURE OF A FULLY FUNCTIONAL LACCASE FROM THE LIGNINOL... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2xyb | |||||||||
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Title | CRYSTAL STRUCTURE OF A FULLY FUNCTIONAL LACCASE FROM THE LIGNINOLYTIC FUNGUS PYCNOPORUS CINNABARINUS | |||||||||
![]() | LACCASE | |||||||||
![]() | OXIDOREDUCTASE / BLUE MULTI-COPPER OXIDASE / PHENOL OXIDASE / LIGNIN DEGRADATION | |||||||||
Function / homology | ![]() hydroquinone:oxygen oxidoreductase activity / laccase / copper ion binding / extracellular region Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Piontek, K. / Choinowski, T. / Antorini, M. / Herpoel-Gimbert, I. / Plattner, D.A. / Sigoillot, J.C. / Asther, M. / Winterhalter, K. | |||||||||
![]() | ![]() Title: Substrate Binding and Copper Geometry in Laccases Authors: Piontek, K. / Choinowski, T. / Antorini, M. / Herpoel-Gimbert, I. / Asther, M. / Plattner, D.A. #1: Journal: Biochim.Biophys.Acta / Year: 2002 Title: Purification, Crystallisation and X-Ray Diffraction Study of Fully Functional Laccases from Two Ligninolytic Fungi. Authors: Antorini, M. / Herpoel-Gimbert, I. / Choinowski, T. / Sigoillot, J. / Asther, M. / Winterhalter, K. / Piontek, K. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 140.1 KB | Display | ![]() |
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PDB format | ![]() | 104.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 29.8 KB | Display | |
Data in CIF | ![]() | 46.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1gycS S: Starting model for refinement |
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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 on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 54001.773 Da / Num. of mol.: 1 / Fragment: RESIDUES 22-518 / Source method: isolated from a natural source Details: THIS ORGANISM IS ALSO KNOWN AS CINNABAR-RED POLYPORE Source: (natural) ![]() |
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-Sugars , 4 types, 5 molecules ![](data/chem/img/NAG.gif)
#2: Polysaccharide | alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||||
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#3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #7: Sugar | ChemComp-NAG / | |
-Non-polymers , 9 types, 734 molecules ![](data/chem/img/CU.gif)
![](data/chem/img/PER.gif)
![](data/chem/img/AS8.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PER.gif)
![](data/chem/img/AS8.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-CU / #6: Chemical | ChemComp-PER / | #8: Chemical | ChemComp-AS8 / | #9: Chemical | ChemComp-ACT / | #10: Chemical | #11: Chemical | ChemComp-GOL / #12: Chemical | ChemComp-ZN / #13: Chemical | ChemComp-NA / | #14: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.5 % / Description: NONE |
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Crystal grow | pH: 5.9 Details: 12.0 MG/ML PROTEIN, 14 % PEG 8000, 20 % GLYCEROL, 160 MM ZN-ACETATE, 5 MM CU-SULAFTE, 100 MM NA-CACODYLATE, PH 5.9 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Aug 13, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8499 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→50 Å / Num. obs: 66427 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 25.6 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 27.4 |
Reflection shell | Resolution: 1.75→1.79 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 1.3 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1GYC Resolution: 1.75→72.55 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.702 / SU ML: 0.054 / Cross valid method: THROUGHOUT / ESU R: 0.097 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE ASSIGNMENT OF LIGAND UVW BOUND AT THE PROPOSED SUBSTRATE BINDING SITE IS PROVISIONAL. A CHEMICAL CONFIRMATION HAS NOT BEEN DONE. THE ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE ASSIGNMENT OF LIGAND UVW BOUND AT THE PROPOSED SUBSTRATE BINDING SITE IS PROVISIONAL. A CHEMICAL CONFIRMATION HAS NOT BEEN DONE. THE CHARACTERIZATION OF THIS LIGAND HAS BEEN MERELY BASED ON ITS CHEMICAL ENVIRONMENT AND THE ELECTRON DENSITY.
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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: 32.752 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→72.55 Å
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Refine LS restraints |
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