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- PDB-2yyg: Crystal structure of the oxygenase component (HpaB) of 4-hydroxyp... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2yyg | ||||||
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Title | Crystal structure of the oxygenase component (HpaB) of 4-hydroxyphenylacetate 3-monooxygenase | ||||||
![]() | 4-hydroxyphenylacetate-3-hydroxylase | ||||||
![]() | OXIDOREDUCTASE / Structurome / RIKEN SPring-8 Center / oxygnase component / 4-hydroxyphenylacetate 3-monooxygenase / two-component flavin diffusible monooxygenase | ||||||
Function / homology | ![]() 4-hydroxyphenylacetate 3-monooxygenase / 4-hydroxyphenylacetate 3-monooxygenase activity / phenylacetate catabolic process / oxidoreductase activity, acting on the CH-CH group of donors / flavin adenine dinucleotide binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kim, S.-H. / Hisano, T. / Takeda, K. / Iwasaki, W. / Ebihara, A. / Miki, K. | ||||||
![]() | ![]() Title: Crystal Structure of the Oxygenase Component (HpaB) of the 4-Hydroxyphenylacetate 3-Monooxygenase from Thermus thermophilus HB8 Authors: Kim, S.-H. / Hisano, T. / Takeda, K. / Iwasaki, W. / Ebihara, A. / Miki, K. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2007 Title: Crystallization and preliminary X-ray analysis of the oxygenase component (HpaB) of 4-hydroxyphenylacetate 3-monooxygenase from Thermus thermophilus HB8 Authors: Kim, S.-H. / Miyatake, H. / Hisano, T. / Iwasaki, W. / Ebihara, A. / Miki, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 113.1 KB | Display | ![]() |
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PDB format | ![]() | 86 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 443 KB | Display | ![]() |
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Full document | ![]() | 447.6 KB | Display | |
Data in XML | ![]() | 22.3 KB | Display | |
Data in CIF | ![]() | 33.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2yyiC ![]() 2yyjC ![]() 2yykSC ![]() 2yylC ![]() 2yymC 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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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 54369.043 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||
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#2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 55.11 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 1.5M ammonium sulfate, 0.1M Tris-HCl, 25% (v/v) glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 21, 2005 / Details: mirrors |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→47.01 Å / Num. all: 38621 / Num. obs: 38621 / Redundancy: 4.3 % / Biso Wilson estimate: 25.304 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 22.3 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.165 / Num. unique all: 3220 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2YYK Resolution: 2→47.01 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 32.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→47.01 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: 6
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