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Yorodumi- PDB-5frz: crystal structure of the phenol-responsive sensory domain of the ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5frz | ||||||
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Title | crystal structure of the phenol-responsive sensory domain of the transcription activator PoxR with 3,4-dimethylphenol | ||||||
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: 2.1 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5frz.cif.gz | 88.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5frz.ent.gz | 67.6 KB | Display | PDB format |
PDBx/mmJSON format | 5frz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5frz_validation.pdf.gz | 442.8 KB | Display | wwPDB validaton report |
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Full document | 5frz_full_validation.pdf.gz | 448.8 KB | Display | |
Data in XML | 5frz_validation.xml.gz | 17.6 KB | Display | |
Data in CIF | 5frz_validation.cif.gz | 23.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fr/5frz ftp://data.pdbj.org/pub/pdb/validation_reports/fr/5frz | HTTPS FTP |
-Related structure data
Related structure data | 5fruC 5frvC 5frwC 5frxC 5fryC 5fs0C 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: 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 / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.81 Å3/Da / Density % sol: 31.94 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 287 K |
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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: 1.64→50 Å / Num. obs: 41911 / % possible obs: 98 % / Observed criterion σ(I): -3 / Redundancy: 13.6 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 57.21 |
Reflection shell | Resolution: 1.64→1.67 Å / Redundancy: 11.7 % / Rmerge(I) obs: 0.97 / Mean I/σ(I) obs: 2.45 / % possible all: 99.5 |
-Processing
Software | Name: PHENIX / Version: (PHENIX.REFINE: 1.9_1692) / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MIR Starting model: NONE Resolution: 2.1→22.926 Å / SU ML: 0.27 / σ(F): 1.33 / Phase error: 29.96 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→22.926 Å
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Refine LS restraints |
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LS refinement shell |
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