[English] 日本語
Yorodumi- PDB-5bpx: Structure of the 2,4'-dihydroxyacetophenone dioxygenase from Alca... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5bpx | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of the 2,4'-dihydroxyacetophenone dioxygenase from Alcaligenes sp. 4HAP. | ||||||
Components | 2,4'-dihydroxyacetophenone dioxygenase | ||||||
Keywords | OXIDOREDUCTASE / rmlc-like cupin protein | ||||||
Function / homology | Function and homology information 2,4'-dihydroxyacetophenone dioxygenase / 2,4'-dihydroxyacetophenone dioxygenase activity / metal ion binding Similarity search - Function | ||||||
Biological species | Alcaligenes sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å | ||||||
Authors | Guo, J. / Erskine, P. / Wood, S.P. / Cooper, J.B. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2015 Title: Extension of resolution and oligomerization-state studies of 2,4'-dihydroxyacetophenone dioxygenase from Alcaligenes sp. 4HAP. Authors: Guo, J. / Erskine, P. / Coker, A.R. / Gor, J. / Perkins, S.J. / Wood, S.P. / Cooper, J.B. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5bpx.cif.gz | 51 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5bpx.ent.gz | 34.7 KB | Display | PDB format |
PDBx/mmJSON format | 5bpx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5bpx_validation.pdf.gz | 443.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5bpx_full_validation.pdf.gz | 444.8 KB | Display | |
Data in XML | 5bpx_validation.xml.gz | 10.2 KB | Display | |
Data in CIF | 5bpx_validation.cif.gz | 14 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bp/5bpx ftp://data.pdbj.org/pub/pdb/validation_reports/bp/5bpx | HTTPS FTP |
-Related structure data
Related structure data | 4p9gS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 17743.848 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: A catalytic ferrous ion is tightly bound in the active site. Source: (gene. exp.) Alcaligenes sp. (bacteria) / Gene: dad / Production host: Escherichia coli (E. coli) References: UniProt: Q9REI7, 2,4'-dihydroxyacetophenone dioxygenase |
---|---|
#2: Chemical | ChemComp-FE / |
#3: Chemical | ChemComp-ACT / |
#4: Chemical | ChemComp-GOL / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.82 Å3/Da / Density % sol: 56.34 % / Description: long needles |
---|---|
Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.3 Details: 0.1 M sodium cacodylate pH 5.9 - 6.8. 1.1 - 1.6 M sodium acetate PH range: 5.9 - 6.8 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 29, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 1.88→41.62 Å / Num. obs: 19556 / % possible obs: 99.5 % / Redundancy: 20.3 % / Rmerge(I) obs: 0.122 / Net I/σ(I): 21.8 |
Reflection shell | Resolution: 1.88→1.93 Å / Redundancy: 19.5 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 5 / % possible all: 99 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4p9g Resolution: 1.88→41.62 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.911 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.09 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.147 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.88→41.62 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|