[English] 日本語
Yorodumi- PDB-2qa2: Crystal structure of CabE, an aromatic hydroxylase from angucycli... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2qa2 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of CabE, an aromatic hydroxylase from angucycline biosynthesis, determined to 2.7 A resolution | ||||||
Components | Polyketide oxygenase CabE | ||||||
Keywords | OXIDOREDUCTASE / FAD / angucycline / polyketide / aromatic hydroxylase | ||||||
Function / homology | Function and homology information Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With NADH or NADPH as one donor, and incorporation of one atom of oxygen into the other donor / FAD binding Similarity search - Function | ||||||
Biological species | Streptomyces (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Koskiniemi, H. / Dobritzsch, D. / Metsa-Ketela, M. / Kallio, P. / Niemi, J. / Schneider, G. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 Title: Crystal structures of two aromatic hydroxylases involved in the early tailoring steps of angucycline biosynthesis Authors: Koskiniemi, H. / Metsa-Ketela, M. / Dobritzsch, D. / Kallio, P. / Korhonen, H. / Mantsala, P. / Schneider, G. / Niemi, J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2qa2.cif.gz | 108.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2qa2.ent.gz | 81.6 KB | Display | PDB format |
PDBx/mmJSON format | 2qa2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qa/2qa2 ftp://data.pdbj.org/pub/pdb/validation_reports/qa/2qa2 | HTTPS FTP |
---|
-Related structure data
Related structure data | 2qa1SC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Details | The biological unit is a dimer generated from the monomer in the asymmetric unit by the operation 1 0 0 0-1 0 0 0-1 |
-Components
#1: Protein | Mass: 53639.438 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces (bacteria) / Genus: Streptomyces / Strain: sp. H021 / Gene: cabe / Plasmid: pBHB / Production host: Escherichia coli (E. coli) / Strain (production host): TOP10 References: UniProt: D0VWY3*PLUS, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With NADH or NADPH as one donor, and incorporation of one atom of ...References: UniProt: D0VWY3*PLUS, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With NADH or NADPH as one donor, and incorporation of one atom of oxygen into the other donor |
---|---|
#2: Chemical | ChemComp-FAD / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.98 Å3/Da / Density % sol: 69.06 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 20 % PEG 3350, 0.1M bis-tris propane, 0.2M Na/K-phosphate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.84 |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Feb 24, 2006 |
Radiation | Monochromator: Si [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.84 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→30 Å / Num. all: 24379 / Num. obs: 24379 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 50.7 Å2 / Rmerge(I) obs: 0.097 / Rsym value: 0.097 / Net I/σ(I): 16.22 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.518 / Mean I/σ(I) obs: 4 / Num. unique all: 2467 / Rsym value: 0.518 / % possible all: 99.9 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2QA1 Resolution: 2.7→29.83 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.908 / SU B: 35.281 / SU ML: 0.32 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.437 / ESU R Free: 0.304 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: The analysis of the intensity distribution suggests possible twinning. Refinement using the twin protocol did however not improve Rfree and the crystals were therefore not considered twinned ...Details: The analysis of the intensity distribution suggests possible twinning. Refinement using the twin protocol did however not improve Rfree and the crystals were therefore not considered twinned with space group P6522. Furthermore, data processing using programs other than XDS did not show signs of twinning.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 72.281 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→29.83 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.7→2.77 Å / Total num. of bins used: 20
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|