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- PDB-6kli: Crystal Structure of the Zea Mays laccase 3 complexed with sinapyl -
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Open data
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Basic information
Entry | Database: PDB / ID: 6kli | |||||||||
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Title | Crystal Structure of the Zea Mays laccase 3 complexed with sinapyl | |||||||||
![]() | Laccase | |||||||||
![]() | OXIDOREDUCTASE | |||||||||
Function / homology | ![]() lignin catabolic process / hydroquinone:oxygen oxidoreductase activity / laccase / apoplast / copper ion binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() ![]() | |||||||||
![]() | Xie, T. / Liu, Z.C. / Wang, G.G. | |||||||||
![]() | ![]() Title: Structural basis for monolignol oxidation by a maize laccase. Authors: Xie, T. / Liu, Z. / Wang, G. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 139.7 KB | Display | ![]() |
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PDB format | ![]() | 104.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 26.2 KB | Display | |
Data in CIF | ![]() | 39.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6klgC ![]() 6kljC ![]() 1aozS C: citing same article ( 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: 61397.008 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Sugars , 2 types, 7 molecules ![](data/chem/img/NAG.gif)
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Sugar | ChemComp-NAG / |
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-Non-polymers , 5 types, 472 molecules ![](data/chem/img/CU.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/55B.gif)
![](data/chem/img/OXY.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/55B.gif)
![](data/chem/img/OXY.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-CU / #5: Chemical | ChemComp-GOL / | #6: Chemical | ChemComp-55B / | #7: Chemical | ChemComp-OXY / | #8: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.07 Å3/Da / Density % sol: 59.96 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 5% of PEG 3350, 0.2 M (NH4)2SO4 and 0.1 M Bis-tris,pH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 15, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97853 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→24.7 Å / Num. obs: 71621 / % possible obs: 99.4 % / Redundancy: 8.4 % / Biso Wilson estimate: 20.97 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.08 / Net I/σ(I): 26.8 |
Reflection shell | Resolution: 1.8→1.83 Å / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 5 / Num. unique obs: 3480 / CC1/2: 0.925 |
-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1AOZ Resolution: 1.8→24.678 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.53
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 62.38 Å2 / Biso mean: 24.4768 Å2 / Biso min: 11.94 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.8→24.678 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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