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Yorodumi- PDB-7a8v: Crystal structure of Polysaccharide monooxygenase from P.verruculosum -
+Open data
-Basic information
Entry | Database: PDB / ID: 7a8v | ||||||
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Title | Crystal structure of Polysaccharide monooxygenase from P.verruculosum | ||||||
Components | Lytic polysaccharide monooxygenase | ||||||
Keywords | OXIDOREDUCTASE / MONOOXYGENASE / P.verruculosum | ||||||
Function / homology | Auxiliary Activity family 9 / Auxiliary Activity family 9 (formerly GH61) / monooxygenase activity / extracellular region / COPPER (II) ION / alpha-D-mannopyranose / Lytic polysaccharide monooxygenase Function and homology information | ||||||
Biological species | Talaromyces verruculosus (fungus) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.94961087137 Å | ||||||
Authors | Nemashkalov, V. / Kravchenko, O. / Gabdulkhakov, A. / Tischenko, S. / Rozhkova, A. / Sinitsyn, A. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: Crystal structure of Polysaccharide monooxygenase from P.verruculosum Authors: Nemashkalov, V. / Kravchenko, O. / Gabdulkhakov, A. / Tischenko, S. / Rozhkova, A. / Sinitsyn, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7a8v.cif.gz | 68.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7a8v.ent.gz | 47.6 KB | Display | PDB format |
PDBx/mmJSON format | 7a8v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7a8v_validation.pdf.gz | 4.1 MB | Display | wwPDB validaton report |
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Full document | 7a8v_full_validation.pdf.gz | 4.1 MB | Display | |
Data in XML | 7a8v_validation.xml.gz | 13.5 KB | Display | |
Data in CIF | 7a8v_validation.cif.gz | 20.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a8/7a8v ftp://data.pdbj.org/pub/pdb/validation_reports/a8/7a8v | HTTPS FTP |
-Related structure data
Related structure data | 4eisS S: Starting model for refinement |
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Similar structure data |
-Links
-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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 24367.729 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Talaromyces verruculosus (fungus) / Gene: lpmo1 / Production host: Penicillium canescens (fungus) / References: UniProt: A0A482A9N4 |
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-Sugars , 2 types, 8 molecules
#2: Sugar | #3: Sugar | ChemComp-MAN / |
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-Non-polymers , 3 types, 261 molecules
#4: Chemical | #5: Chemical | ChemComp-CU / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.13 Å3/Da / Density % sol: 70.24 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / Details: cobalt chloride, MES, ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 110 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å |
Detector | Type: Bruker Platinum 135 / Detector: CCD / Date: Apr 16, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.94→33.04 Å / Num. obs: 29254 / % possible obs: 99 % / Redundancy: 4.04 % / Biso Wilson estimate: 10.7624280739 Å2 / Rmerge(I) obs: 0.1038 / Net I/σ(I): 10.28 |
Reflection shell | Resolution: 1.95→2.05 Å / Rmerge(I) obs: 0.2844 / Num. unique obs: 3860 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4EIS Resolution: 1.94961087137→33.03625 Å / SU ML: 0.173506366293 / Cross valid method: FREE R-VALUE / σ(F): 1.34760157227 / Phase error: 16.3330556472 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.3679876308 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.94961087137→33.03625 Å
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Refine LS restraints |
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LS refinement shell |
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