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- PDB-7ptz: High resolution X-ray structure of E. coli expressed Lentinus sim... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7ptz | ||||||||||||
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Title | High resolution X-ray structure of E. coli expressed Lentinus similis LPMO. | ||||||||||||
![]() | Auxiliary activity 9 | ||||||||||||
![]() | CARBOHYDRATE / LPMO / Monooxygenase / high resolution / Auxillary activity | ||||||||||||
Function / homology | ![]() cellulose binding / cellulase / cellulase activity / cellulose catabolic process / extracellular region / metal ion binding Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Banerjee, S. / Muderspach, S.J. / Tandrup, T. / Ipsen, J.O. / Hernandez-Rollan, C. / Norholm, H.H.M. / Johansen, K.S. / Lo Leggio, L. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Protonation State of an Important Histidine from High Resolution Structures of Lytic Polysaccharide Monooxygenases. Authors: Banerjee, S. / Muderspach, S.J. / Tandrup, T. / Frandsen, K.E.H. / Singh, R.K. / Ipsen, J.O. / Hernandez-Rollan, C. / Norholm, M.H.H. / Bjerrum, M.J. / 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 | ![]() | 115.3 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.5 MB | Display | ![]() |
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Full document | ![]() | 2.5 MB | Display | |
Data in XML | ![]() | 14.7 KB | Display | |
Data in CIF | ![]() | 23.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7pu1C ![]() 7pqrS 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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Unit cell |
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Components
#1: Protein | Mass: 25259.832 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: Chemical | ChemComp-CL / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 52.63 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 3.5 / Details: 0.1 M citric acid pH 3.5 and 3.0 M NaCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 15, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.09→48.5 Å / Num. obs: 96541 / % possible obs: 91.3 % / Redundancy: 11.99 % / CC1/2: 0.99 / Rrim(I) all: 0.059 / Net I/σ(I): 19.3 |
Reflection shell | Resolution: 1.09→1.16 Å / Num. unique obs: 10733 / CC1/2: 0.73 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7PQR Resolution: 1.093→48.5 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.984 / WRfactor Rfree: 0.144 / WRfactor Rwork: 0.124 / SU B: 0.814 / SU ML: 0.017 / Average fsc free: 0.9402 / Average fsc work: 0.9418 / Cross valid method: FREE R-VALUE / ESU R: 0.025 / ESU R Free: 0.025 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: 17.228 Å2
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Refinement step | Cycle: LAST / Resolution: 1.093→48.5 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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