+Open data
-Basic information
Entry | Database: PDB / ID: 4rns | ||||||
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Title | PcpR inducer binding domain (apo-form) | ||||||
Components | PCP degradation transcriptional activation protein | ||||||
Keywords | TRANSCRIPTION / LysR family transcriptional regulator | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Sphingobium chlorophenolicum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Hayes, R.P. / Moural, T.W. / Lewis, K.M. / Onofrei, D. / Xun, L. / Kang, C. | ||||||
Citation | Journal: Int J Mol Sci / Year: 2014 Title: Structures of the Inducer-Binding Domain of Pentachlorophenol-Degrading Gene Regulator PcpR from Sphingobium chlorophenolicum. Authors: Hayes, R.P. / Moural, T.W. / Lewis, K.M. / Onofrei, D. / Xun, L. / Kang, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4rns.cif.gz | 178.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4rns.ent.gz | 144.2 KB | Display | PDB format |
PDBx/mmJSON format | 4rns.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rn/4rns ftp://data.pdbj.org/pub/pdb/validation_reports/rn/4rns | HTTPS FTP |
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-Related structure data
Related structure data | 4rpnC 4rpoC 2y7wS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 25354.889 Da / Num. of mol.: 4 / Fragment: residues 85-307 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sphingobium chlorophenolicum (bacteria) Gene: pcpR / Production host: Escherichia coli (E. coli) / References: UniProt: P52679 #2: Water | ChemComp-HOH / | |
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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: 2.99 Å3/Da / Density % sol: 58.89 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.2 M sodium tartrate dibasic dihydrate, 20% w/v polyethylene glycol 3,350, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å | |||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 1, 2012 | |||||||||||||||||||||
Radiation | Monochromator: KOHZU / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 2.7→50 Å / Num. all: 307311 / Num. obs: 57389 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.139 | |||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2Y7W Resolution: 2.7→42.362 Å / SU ML: 0.31 / σ(F): 1.97 / Phase error: 23.13 / 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: 2.7→42.362 Å
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Refine LS restraints |
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LS refinement shell |
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