[English] 日本語
Yorodumi- PDB-5ux2: Protein 19 with aldehyde deformylating oxidase activity from Syne... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ux2 | ||||||
---|---|---|---|---|---|---|---|
Title | Protein 19 with aldehyde deformylating oxidase activity from Synechococcus | ||||||
Components | Aldehyde decarbonylase | ||||||
Keywords | LYASE / decarbonylase / iron / ferritin | ||||||
Function / homology | Function and homology information aldehyde oxygenase (deformylating) / : / : / transition metal ion binding Similarity search - Function | ||||||
Biological species | Synechococcus sp. RS9917 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å | ||||||
Authors | Wilson, D.K. / Mak, W.S. / Siegel, J.B. | ||||||
Citation | Journal: To Be Published Title: Protein 19 with aldehyde deformylating oxidase activity from Synechococcus Authors: Wilson, D.K. / Mak, W.S. / Siegel, J.B. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5ux2.cif.gz | 100 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5ux2.ent.gz | 75.5 KB | Display | PDB format |
PDBx/mmJSON format | 5ux2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ux2_validation.pdf.gz | 448.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5ux2_full_validation.pdf.gz | 450.5 KB | Display | |
Data in XML | 5ux2_validation.xml.gz | 16.8 KB | Display | |
Data in CIF | 5ux2_validation.cif.gz | 22.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ux/5ux2 ftp://data.pdbj.org/pub/pdb/validation_reports/ux/5ux2 | HTTPS FTP |
-Related structure data
Related structure data | 5uw2S S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 26285.074 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechococcus sp. RS9917 (bacteria) / Gene: RS9917_12945 / Production host: Escherichia coli (E. coli) References: UniProt: A3Z6M0, aldehyde oxygenase (deformylating) #2: Chemical | ChemComp-FE / #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.45 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 25.9 mg/ml 17% PEG 4000, 8.5 isopropanol, 85 mM Hepes |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 13, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 1.99→109.06 Å / Num. obs: 33222 / % possible obs: 95.3 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 11.9 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5UW2 Resolution: 1.99→109.06 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.926 / SU B: 5.522 / SU ML: 0.151 / Cross valid method: THROUGHOUT / ESU R: 0.191 / ESU R Free: 0.172 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.704 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.99→109.06 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|