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Yorodumi- PDB-6tbr: Glycosylated AA13 Lytic polysaccharide monooxygenase from Aspergi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6tbr | ||||||||||||
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Title | Glycosylated AA13 Lytic polysaccharide monooxygenase from Aspergillus oryzae in P1 space group | ||||||||||||
Components | AoAA13 | ||||||||||||
Keywords | OXIDOREDUCTASE / beta-sandwich fold / glycosylated / P1 | ||||||||||||
Function / homology | Cellulose/chitin-binding protein, N-terminal / Lytic polysaccharide mono-oxygenase, cellulose-degrading / membrane / metal ion binding / Inactive AA13 family lytic polysaccharide monooxygenase Function and homology information | ||||||||||||
Biological species | Aspergillus oryzae RIB40 (mold) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.7 Å | ||||||||||||
Authors | Frandsen, K.E.H. / Muderspach, S.J. / Tandrup, T. / Poulsen, J.C.N. / Lo Leggio, L. | ||||||||||||
Funding support | Denmark, 3items
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Citation | Journal: Amylase / Year: 2019 Title: Further structural studies of the lytic polysaccharide monooxygenase AoAA13 belonging to the starch-active AA13 family Authors: Muderspach, S.J. / Tandrup, T. / Frandsen, K.E.H. / Santoni, G. / Poulsen, J.C.N. / Lo Leggio, L. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6tbr.cif.gz | 116 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6tbr.ent.gz | 93.3 KB | Display | PDB format |
PDBx/mmJSON format | 6tbr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6tbr_validation.pdf.gz | 440.9 KB | Display | wwPDB validaton report |
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Full document | 6tbr_full_validation.pdf.gz | 444 KB | Display | |
Data in XML | 6tbr_validation.xml.gz | 25.4 KB | Display | |
Data in CIF | 6tbr_validation.cif.gz | 38.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tb/6tbr ftp://data.pdbj.org/pub/pdb/validation_reports/tb/6tbr | HTTPS FTP |
-Related structure data
-Links
-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: 25691.057 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aspergillus oryzae RIB40 (mold) / Gene: AO090701000246 / Production host: Aspergillus oryzae (mold) / References: UniProt: Q2U8Y3 #2: Chemical | ChemComp-ZN / #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.39 Å3/Da / Density % sol: 48.55 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.01 M ZnCl2, 14% PEG6000, 0.1 M MES pH 6.0, 30% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.04 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jun 7, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.04 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→53.84 Å / Num. obs: 48576 / % possible obs: 92.6 % / Redundancy: 1.68 % / CC1/2: 0.994 / Rrim(I) all: 0.077 / Net I/σ(I): 2.87 |
Reflection shell | Resolution: 1.7→1.74 Å / Mean I/σ(I) obs: 9.04 / Num. unique obs: 3521 / CC1/2: 0.877 / Rrim(I) all: 0.455 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.7→53.84 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.914 / SU B: 2.745 / SU ML: 0.091 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.13 / ESU R Free: 0.133
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 51.89 Å2 / Biso mean: 17.756 Å2 / Biso min: 2.34 Å2
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Refinement step | Cycle: final / Resolution: 1.7→53.84 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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