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Open data
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Basic information
Entry | Database: PDB / ID: 6z5y | ||||||
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Title | Structure of a novel LPMO from Phytophthora infestans | ||||||
![]() | Lytic Polysaccharide Monooxygenase | ||||||
![]() | METAL BINDING PROTEIN / Lytic polysaccharide monooxygenase / copper / LPMO | ||||||
Function / homology | COPPER (II) ION / TRIETHYLENE GLYCOL / Uncharacterized protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Urresti, S. / Davies, G.J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Secreted pectin monooxygenases drive plant infection by pathogenic oomycetes. Authors: Sabbadin, F. / Urresti, S. / Henrissat, B. / Avrova, A.O. / Welsh, L.R.J. / Lindley, P.J. / Csukai, M. / Squires, J.N. / Walton, P.H. / Davies, G.J. / Bruce, N.C. / Whisson, S.C. / McQueen-Mason, S.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 163.4 KB | Display | ![]() |
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PDB format | ![]() | 134.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 264 KB | Display | ![]() |
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Full document | ![]() | 267.6 KB | Display | |
Data in XML | ![]() | 9.4 KB | Display | |
Data in CIF | ![]() | 15.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 20016.531 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: C-terminus Strep tag sequence: WSHPQFEK Source: (gene. exp.) ![]() Gene: PITG_04949 / Production host: ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-PGE / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.18 % / Description: Hollow rods |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 20mM Tris pH 7.0, 22% Polyethylene Glycol (PEG) 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 1, 2018 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.916 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.01→28.79 Å / Num. obs: 156702 / % possible obs: 92.4 % / Redundancy: 3.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.03 / Rrim(I) all: 0.057 / Net I/σ(I): 8.9 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: AB INITIO PHASING / Resolution: 1.01→28.79 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.973 / SU B: 0.791 / SU ML: 0.018 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.025 / ESU R Free: 0.025 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY Residues 139-142 and 172-177 (chains A and B) show poor density and therefore low occupancy. C-terminal ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY Residues 139-142 and 172-177 (chains A and B) show poor density and therefore low occupancy. C-terminal residues (172-177) correspond to a non cleaved Strep tag, and some have been built with no side chains.
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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: 36.26 Å2 / Biso mean: 11.889 Å2 / Biso min: 5.72 Å2
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Refinement step | Cycle: final / Resolution: 1.01→28.79 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.01→1.036 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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