[English] 日本語
Yorodumi- PDB-5frx: crystal structure of the phenol-responsive sensory domain of the ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5frx | ||||||
---|---|---|---|---|---|---|---|
Title | crystal structure of the phenol-responsive sensory domain of the transcription activator PoxR in complex with 4-nitrophenol | ||||||
Components | Positive phenol-degradative gene regulator | ||||||
Keywords | TRANSCRIPTION / PHENOL / DMPR / ENHANCER-BINDING PROTEIN / ACTIVATOR / ATPASE FAMILY | ||||||
Function / homology | Function and homology information sequence-specific DNA binding / regulation of DNA-templated transcription / ATP hydrolysis activity / ATP binding / identical protein binding / metal ion binding Similarity search - Function | ||||||
Biological species | Ralstonia sp. E2 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.4 Å | ||||||
Authors | Patil, V.V. / Woo, E.J. | ||||||
Citation | Journal: Structure / Year: 2016 Title: Structural Analysis of the Phenol-Responsive Sensory Domain of the Transcription Activator Poxr Authors: Patil, V.V. / Park, K.-H. / Lee, S.-G. / Woo, E.J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5frx.cif.gz | 89.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5frx.ent.gz | 68 KB | Display | PDB format |
PDBx/mmJSON format | 5frx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5frx_validation.pdf.gz | 418.5 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5frx_full_validation.pdf.gz | 429.5 KB | Display | |
Data in XML | 5frx_validation.xml.gz | 11.9 KB | Display | |
Data in CIF | 5frx_validation.cif.gz | 16.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fr/5frx ftp://data.pdbj.org/pub/pdb/validation_reports/fr/5frx | HTTPS FTP |
-Related structure data
Related structure data | 5fruC 5frvC 5frwC 5fryC 5frzC 5fs0C C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 23495.096 Da / Num. of mol.: 2 / Fragment: PHENOL BINDING DOMAIN, UNP RESIDUES 1-211 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ralstonia sp. E2 (bacteria) / Gene: poxR / Variant: E2 / Plasmid: pET22B-CPD / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O84957 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 1.82 Å3/Da / Density % sol: 32.58 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.18 M potassium chloride, 0.01 M magnesium sulfate heptahydrate, 0.05 M MES monohydrate (pH 5.6) |
-Data collection
Diffraction | Mean temperature: 287 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→50 Å / Num. obs: 19340 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 13.5 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 46.79 |
Reflection shell | Resolution: 2.15→2.19 Å / Redundancy: 9.5 % / Rmerge(I) obs: 0.976 / Mean I/σ(I) obs: 2.46 / % possible all: 100 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MIR Starting model: NONE Resolution: 2.4→36.29 Å / SU ML: 0.32 / σ(F): 1.34 / Phase error: 31.81 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→36.29 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|