[English] 日本語
Yorodumi- PDB-5kbi: CRYSTAL STRUCTURE OF THE AROMATIC SENSOR DOMAIN OF MOPR IN COMPLE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5kbi | ||||||
---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF THE AROMATIC SENSOR DOMAIN OF MOPR IN COMPLEX WITH CATACHOL | ||||||
Components | MopR | ||||||
Keywords | TRANSCRIPTION / AROMATIC SENSOR | ||||||
Function / homology | Function and homology information sequence-specific DNA binding / regulation of DNA-templated transcription / ATP hydrolysis activity / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Acinetobacter calcoaceticus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9 Å | ||||||
Authors | Ray, S. / Anand, R. / Panjikar, S. | ||||||
Citation | Journal: Acs Chem.Biol. / Year: 2016 Title: Structural Basis of Selective Aromatic Pollutant Sensing by the Effector Binding Domain of MopR, an NtrC Family Transcriptional Regulator. Authors: Ray, S. / Gunzburg, M.J. / Wilce, M. / Panjikar, S. / Anand, R. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5kbi.cif.gz | 93.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5kbi.ent.gz | 70.6 KB | Display | PDB format |
PDBx/mmJSON format | 5kbi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5kbi_validation.pdf.gz | 461.8 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5kbi_full_validation.pdf.gz | 472.2 KB | Display | |
Data in XML | 5kbi_validation.xml.gz | 17.4 KB | Display | |
Data in CIF | 5kbi_validation.cif.gz | 22.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kb/5kbi ftp://data.pdbj.org/pub/pdb/validation_reports/kb/5kbi | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.9264, -0.3728, 0.05224), Vector: |
-Components
#1: Protein | Mass: 26387.182 Da / Num. of mol.: 2 / Fragment: SENSOR DOMAIN, RESIDUES 1-229 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter calcoaceticus (bacteria) / Gene: mopR / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: Q43965 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.49 % / Description: needle shape |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7.6 Details: 0.1 M LISO4, 12% W/V PEG 6000, 0.1M TRI-SODIUM CITRATE (PH 5.6) PH range: 7.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 11, 2014 / Details: MIRROR |
Radiation | Monochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→20 Å / Num. obs: 11761 / % possible obs: 99.1 % / Observed criterion σ(I): 2 / Redundancy: 4.35 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 11.62 |
Reflection shell | Resolution: 2.9→2.95 Å / Redundancy: 4.42 % / Rmerge(I) obs: 0.83 / Mean I/σ(I) obs: 2.49 / % possible all: 97.5 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 2.9→19.98 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.857 / SU B: 19.526 / SU ML: 0.367 / Cross valid method: THROUGHOUT / ESU R Free: 0.488 / 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: 49.31 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→19.98 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|