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- PDB-1tzl: Crystal Structure of Pyranose 2-Oxidase from the White-Rot Fungus... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1tzl | ||||||
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Title | Crystal Structure of Pyranose 2-Oxidase from the White-Rot Fungus Peniophora sp. | ||||||
![]() | pyranose oxidase | ||||||
![]() | OXIDOREDUCTASE / GMC oxidoreductase / glucose-methanol-choline family / large inner cavity | ||||||
Function / homology | ![]() pyranose oxidase / pyranose oxidase activity / flavin adenine dinucleotide binding / periplasmic space Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bannwarth, M. / Bastian, S. / Heckmann-Pohl, D. / Giffhorn, F. / Schulz, G.E. | ||||||
![]() | ![]() Title: Crystal structure of pyranose 2-oxidase from the white-rot fungus peniophora sp. Authors: Bannwarth, M. / Bastian, S. / Heckmann-Pohl, D. / Giffhorn, F. / Schulz, G.E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 936.9 KB | Display | ![]() |
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PDB format | ![]() | 803.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.3 MB | Display | ![]() |
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Full document | ![]() | 2.4 MB | Display | |
Data in XML | ![]() | 186.7 KB | Display | |
Data in CIF | ![]() | 258.7 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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Details | Biological assembly is tetramer of chains (A,B,C and D) or (E,F,G and H) |
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Components
#1: Protein | Mass: 70032.930 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-FAD / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: PEG 6000, MES, tributyl phosphine, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 14, 2003 Details: N2 cooled fixed-exit Si(111) monochromator Dynamically bendable mirror | ||||||||||||
Radiation | Monochromator: LN2 cooled fixed-exit Si(111) monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.35→20 Å / Num. all: 228044 / Num. obs: 228044 / % possible obs: 96.1 % / Observed criterion σ(F): 3.99 / Observed criterion σ(I): 3.99 / Redundancy: 2 % / Biso Wilson estimate: 33.7 Å2 / Rmerge(I) obs: 0.092 / Rsym value: 0.066 / Net I/σ(I): 8.42 | ||||||||||||
Reflection shell | Resolution: 2.35→2.42 Å / Redundancy: 2 % / Rmerge(I) obs: 0.295 / Mean I/σ(I) obs: 3.99 / Num. unique all: 35967 / Rsym value: 0.21 / % possible all: 94.9 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.96 Å2
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Refinement step | Cycle: LAST / Resolution: 2.35→19.7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.35→2.41 Å / Total num. of bins used: 20 /
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