[English] 日本語
Yorodumi- PDB-2yyj: Crystal structure of the oxygenase component (HpaB) of 4-hydroxyp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2yyj | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the oxygenase component (HpaB) of 4-hydroxyphenylacetate 3-monooxygenase complexed with FAD and 4-hydroxyphenylacetate | ||||||
Components | 4-hydroxyphenylacetate-3-hydroxylase | ||||||
Keywords | OXIDOREDUCTASE / Structurome / RIKEN SPring-8 Center / oxygnase component / 4-hydroxyphenylacetate 3-monooxygenase / two-component flavin diffusible monooxygenase / FAD and a substrate complex | ||||||
Function / homology | Function and homology information 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 | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å | ||||||
Authors | Kim, S.-H. / Hisano, T. / Takeda, K. / Iwasaki, W. / Ebihara, A. / Miki, K. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2007 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2yyj.cif.gz | 122.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2yyj.ent.gz | 92.6 KB | Display | PDB format |
PDBx/mmJSON format | 2yyj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yy/2yyj ftp://data.pdbj.org/pub/pdb/validation_reports/yy/2yyj | HTTPS FTP |
---|
-Related structure data
Related structure data | 2yygC 2yyiC 2yykSC 2yylC 2yymC C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 54369.043 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5SJP8, EC: 1.14.13.3 | ||||||
---|---|---|---|---|---|---|---|
#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-FAD / | #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.69 Å3/Da / Density % sol: 54.2 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 1 Å |
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: 1.66→46.69 Å / Num. all: 68617 / Num. obs: 68617 / Redundancy: 5.9 % / Biso Wilson estimate: 16.542 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 21.4 |
Reflection shell | Resolution: 1.66→1.72 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.208 / Num. unique all: 6416 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2YYK Resolution: 1.66→46.69 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.3 Å2
| ||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.66→46.69 Å
| ||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6
|