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- PDB-1gyc: CRYSTAL STRUCTURE DETERMINATION AT ROOM TEMPERATURE OF A LACCASE ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1gyc | |||||||||
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Title | CRYSTAL STRUCTURE DETERMINATION AT ROOM TEMPERATURE OF A LACCASE FROM TRAMETES VERSICOLOR IN ITS OXIDISED FORM CONTAINING A FULL COMPLEMENT OF COPPER IONS | |||||||||
![]() | LACCASE 2 | |||||||||
![]() | OXIDOREDUCTASE / LACCASE / DIPHENOL OXIDASE / LIGNIN DEGRADATION | |||||||||
Function / homology | ![]() lignin catabolic process / hydroquinone:oxygen oxidoreductase activity / laccase / copper ion binding / extracellular region Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Choinowski, T. / Antorini, M. / Piontek, K. | |||||||||
![]() | ![]() Title: Crystal Structure of a Laccase from the Fungus Trametes Versicolor at 1.90-A Resolution Containing a Full Complement of Coppers. Authors: Piontek, K. / Antorini, M. / Choinowski, T. #1: Journal: Biochim.Biophys.Acta / Year: 2002 Title: Purificcation, Crystallisation and X-Ray Diffraction Study of Fully Functional Laccases from Two Ligninolytic Fungi Authors: Antorini, M. / Herpoel-Gimbertchoinowski, I. / Sigoillot-C, J. / Asther, M. / Winterhalter, K. | |||||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 130 KB | Display | ![]() |
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PDB format | ![]() | 98.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 460.9 KB | Display | ![]() |
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Full document | ![]() | 464.8 KB | Display | |
Data in XML | ![]() | 2.2 KB | Display | |
Data in CIF | ![]() | 10.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1a65S 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 53677.891 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-Sugars , 2 types, 6 molecules ![](data/chem/img/NAG.gif)
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Sugar | |
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-Non-polymers , 3 types, 596 molecules ![](data/chem/img/CU.gif)
![](data/chem/img/IPA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/IPA.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-CU / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Sequence details | SWISS-PROT ENTRY Q12178 HAS THE CLOSEST AGREEMENT WITH THE SEQUENCE OF THE CRYSTALLIZED STRUCTURE. ...SWISS-PROT ENTRY Q12178 HAS THE CLOSEST AGREEMENT WITH THE SEQUENCE OF THE CRYSTALLIZ |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.53 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 5.6 Details: 20% (W/V) PEG8000, 20% (V/V) ISOPROPANOL, 100 MM SODIUM CITRATE PH 5.6 | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging dropDetails: Antorini, M., (2002) Biochim.Biophys.Acta, 1594, 109. | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 15, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.847 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→20 Å / Num. obs: 52154 / % possible obs: 99.4 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 15.1 |
Reflection | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 20 Å / % possible obs: 99.7 % |
Reflection shell | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 1.97 Å / Rmerge(I) obs: 0.38 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 1A65 Resolution: 1.9→17.9 Å / Details: NONE
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Refinement step | Cycle: LAST / Resolution: 1.9→17.9 Å
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Refinement | *PLUS Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.209 / Rfactor Rwork: 0.168 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 2.02 Å / Rfactor Rfree: 0.257 / Rfactor Rwork: 0.205 / Total num. of bins used: 15 |