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- PDB-7pxt: Structure of an LPMO, collected from serial synchrotron crystallo... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7pxt | |||||||||
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Title | Structure of an LPMO, collected from serial synchrotron crystallography data. | |||||||||
![]() | Auxiliary activity 9 | |||||||||
![]() | OXIDOREDUCTASE / Copper binding protein / Beta-sandwich fold / Auxillary | |||||||||
Function / homology | ![]() cellulose binding / cellulase / cellulase activity / cellulose catabolic process / extracellular region / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Tandrup, T. / Santoni, G. / Lo Leggio, L. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Changes in active-site geometry on X-ray photoreduction of a lytic polysaccharide monooxygenase active-site copper and saccharide binding. Authors: Tandrup, T. / Muderspach, S.J. / Banerjee, S. / Santoni, G. / Ipsen, J.O. / Hernandez-Rollan, C. / Norholm, M.H.H. / Johansen, K.S. / Meilleur, F. / 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 | ![]() | 66.5 KB | Display | ![]() |
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PDB format | ![]() | 46.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 452.5 KB | Display | ![]() |
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Full document | ![]() | 452.4 KB | Display | |
Data in XML | ![]() | 9.7 KB | Display | |
Data in CIF | ![]() | 13.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7pqrC ![]() 7pxiC ![]() 7pxjC ![]() 7pxkC ![]() 7pxlC ![]() 7pxmC ![]() 7pxnC ![]() 7pxrC ![]() 7pxsC ![]() 7pxuC ![]() 7pxvC ![]() 7pxwC ![]() 7pydC ![]() 7pyeC ![]() 7pyfC ![]() 7pygC ![]() 7pyhC ![]() 7pyiC ![]() 7pylC ![]() 7pymC ![]() 7pynC ![]() 7pyoC ![]() 7pypC ![]() 7pyqC ![]() 7pyuC ![]() 7pywC ![]() 7pyxC ![]() 7pyyC ![]() 7pyzC ![]() 7pz0C ![]() 7pz3C ![]() 7pz4C ![]() 7pz5C ![]() 7pz6C ![]() 7pz7C ![]() 7pz8C ![]() 5achS C: citing same article ( 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 on special symmetry positions |
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Components
#1: Protein | Mass: 25272.850 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-CU / |
#3: Sugar | ChemComp-NAG / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.25 Å3/Da / Density % sol: 62.18 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4 Details: 4.1 M NaCl, 0.1 M citric acid pH 4.0 The crystals were equilibrated in a drop of 3.5 M NaCl, 0.1 M citric acid pH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: Y |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI JUNGFRAU 4M / Detector: PIXEL / Date: Nov 15, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→39.69 Å / Num. obs: 21952 / % possible obs: 88 % / Redundancy: 3.51 % / CC1/2: 0.619 / Rrim(I) all: 0.293 / Net I/σ(I): 7.21 |
Reflection shell | Resolution: 2.4→2.46 Å / Redundancy: 3.59 % / Mean I/σ(I) obs: 3.37 / Num. unique obs: 1698 / CC1/2: 0.664 / Rrim(I) all: 0.91 / % possible all: 89.7 |
Serial crystallography sample delivery | Description: mesh and collect routine / Method: fixed target |
Serial crystallography sample delivery fixed target | Sample holding: MicroMesh loop |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5ACH Resolution: 2.4→39.69 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.897 / SU B: 7.629 / SU ML: 0.169 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.319 / ESU R Free: 0.248 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 65.97 Å2 / Biso mean: 21.366 Å2 / Biso min: 0.5 Å2
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Refinement step | Cycle: final / Resolution: 2.4→39.69 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.463 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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