+Open data
-Basic information
Entry | Database: PDB / ID: 7vqf | |||||||||
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Title | Phenol binding protein, MopR | |||||||||
Components | Phenol sensing regulator, MopR | |||||||||
Keywords | DNA BINDING PROTEIN / Transcriptional regulator / phenol | |||||||||
Function / homology | ACETATE ION / PHENOL Function and homology information | |||||||||
Biological species | Acinetobacter calcoaceticus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | |||||||||
Authors | Singh, J. / Ray, S. / Anand, R. | |||||||||
Funding support | India, 2items
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Citation | Journal: J.Biol.Chem. / Year: 2022 Title: Phenol sensing in nature is modulated via a conformational switch governed by dynamic allostery. Authors: Singh, J. / Sahil, M. / Ray, S. / Dcosta, C. / Panjikar, S. / Krishnamoorthy, G. / Mondal, J. / Anand, R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7vqf.cif.gz | 65 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7vqf.ent.gz | 37 KB | Display | PDB format |
PDBx/mmJSON format | 7vqf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7vqf_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 7vqf_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 7vqf_validation.xml.gz | 9.2 KB | Display | |
Data in CIF | 7vqf_validation.cif.gz | 11.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vq/7vqf ftp://data.pdbj.org/pub/pdb/validation_reports/vq/7vqf | HTTPS FTP |
-Related structure data
Related structure data | 5kbeS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 26413.219 Da / Num. of mol.: 1 / Mutation: G148P Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter calcoaceticus (bacteria) / Gene: mopR / Production host: Escherichia coli (E. coli) |
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#2: Chemical | ChemComp-IPH / |
#3: Chemical | ChemComp-ACT / |
#4: Chemical | ChemComp-ZN / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.97 Å3/Da / Density % sol: 37.7 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / Details: 0.2M Mg-acetate.tetrahydrate, 15% w/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 2, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→33.3 Å / Num. obs: 9592 / % possible obs: 99.6 % / Redundancy: 6.1 % / Biso Wilson estimate: 37.99 Å2 / CC1/2: 0.99 / Net I/σ(I): 9.26 |
Reflection shell | Resolution: 2.3→2.4 Å / Num. unique obs: 1769 / CC1/2: 0.86 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5KBE Resolution: 2.3→33.3 Å / SU ML: 0.3313 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.9969 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.79 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→33.3 Å
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Refine LS restraints |
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LS refinement shell |
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