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Open data
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Basic information
Entry | Database: PDB / ID: 8b4g | ||||||||||||
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Title | Structure of a fungal LPMO bound to ligands | ||||||||||||
![]() | Gh61 isozyme a | ||||||||||||
![]() | OXIDOREDUCTASE / Monooxygenase / dihydroxyacetone / Lytic Polysaccharide Monooxygenase / Thermoascus aurantiacus | ||||||||||||
Function / homology | ![]() cellulose binding / cellulase / cellulase activity / cellulose catabolic process / extracellular region / metal ion binding Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Banerjee, S. / Huang, Z. / Brander, S. / Johansen, K.S. / Lo Leggio, L. | ||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Structure of a fungal LPMO bound to ligands Authors: Banerjee, S. / Huang, Z. / Brander, S. / Johansen, K.S. / Lo Leggio, L. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 71.9 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 715.9 KB | Display | ![]() |
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Full document | ![]() | 718.2 KB | Display | |
Data in XML | ![]() | 14.4 KB | Display | |
Data in CIF | ![]() | 21.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3zudS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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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 AAA
#1: Protein | Mass: 24418.043 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Sugars , 2 types, 2 molecules ![](data/chem/img/NAG.gif)
![](data/chem/img/2HA.gif)
![](data/chem/img/2HA.gif)
#3: Sugar | ChemComp-NAG / |
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#5: Sugar | ChemComp-2HA / |
-Non-polymers , 4 types, 280 molecules ![](data/chem/img/CU.gif)
![](data/chem/img/AKR.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/AKR.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-CU / | ||||
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#4: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.81 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1 M HEPES pH 7.5, 20m M MgCl2 and 22 %(w/v) polyacrylic acid 5100 sodium salt |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 X 2M / Detector: PIXEL / Date: Jun 4, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8731 Å / Relative weight: 1 |
Reflection | Resolution: 1.496→87.31 Å / Num. obs: 34235 / % possible obs: 99.3 % / Redundancy: 6.6 % / CC1/2: 0.996 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 1.5→1.52 Å / Num. unique obs: 1426 / CC1/2: 0.509 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3ZUD Resolution: 1.496→43.656 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.964 / WRfactor Rfree: 0.168 / WRfactor Rwork: 0.138 / SU B: 1.575 / SU ML: 0.055 / Average fsc free: 0.9201 / Average fsc work: 0.927 / Cross valid method: FREE R-VALUE / ESU R: 0.068 / ESU R Free: 0.071 Details: Hydrogens have been added in their riding positions
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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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.843 Å2
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Refinement step | Cycle: LAST / Resolution: 1.496→43.656 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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