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Yorodumi- PDB-5kbh: CRYSTAL STRUCTURE OF THE AROMATIC SENSOR DOMAIN OF MOPR IN COMPLE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5kbh | ||||||
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Title | CRYSTAL STRUCTURE OF THE AROMATIC SENSOR DOMAIN OF MOPR IN COMPLEX WITH 3-CHLORO-PHENOL | ||||||
Components | MopRInternational Red Aid | ||||||
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: 2.55 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5kbh.cif.gz | 94.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5kbh.ent.gz | 71.2 KB | Display | PDB format |
PDBx/mmJSON format | 5kbh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kb/5kbh ftp://data.pdbj.org/pub/pdb/validation_reports/kb/5kbh | HTTPS FTP |
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-Related structure data
Related structure data | 5kbeC 5kbgC 5kbiC 5a1e C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-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 / | Sequence details | THIS CRYSTAL STRUCTURE IS A TRUNCATED FORM OF THE PROTEIN WHICH CONTAINS RESIDUES 1-229 | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 50.1 % |
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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 |
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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: 2.55→20 Å / Num. obs: 17367 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 3.79 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 10.48 |
Reflection shell | Resolution: 2.55→2.6 Å / Redundancy: 3.86 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2.31 / % possible all: 97.5 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.55→19.82 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.898 / SU B: 12.824 / SU ML: 0.27 / Cross valid method: THROUGHOUT / ESU R: 0.519 / ESU R Free: 0.312 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50.59 Å2
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Refinement step | Cycle: LAST / Resolution: 2.55→19.82 Å
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