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Yorodumi- PDB-4wlw: CRYSTAL STRUCTURE OF THE AG(I) (ACTIVATOR) FORM OF E. COLI CUER, ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4wlw | ||||||
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Title | CRYSTAL STRUCTURE OF THE AG(I) (ACTIVATOR) FORM OF E. COLI CUER, A COPPER EFFLUX REGULATOR, BOUND TO COPA PROMOTER DNA | ||||||
Components |
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Keywords | TRANSCRIPTION/DNA / PROTEIN-DNA COMPLEX / MERR-FAMILY TRANSCRIPTION REGULATOR / AG(I)FORM / ACTIVATOR / TRANSCRIPTION / TRANSCRIPTION-DNA complex | ||||||
Function / homology | Function and homology information DNA-binding transcription activator activity / cis-regulatory region sequence-specific DNA binding / protein-DNA complex / transcription cis-regulatory region binding / copper ion binding / DNA-binding transcription factor activity / DNA-templated transcription / positive regulation of DNA-templated transcription / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Philips, S.J. / Canalizo-Hernandez, M. / Mondragon, A. / O'Halloran, T.V. | ||||||
Funding support | United States, 1items
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Citation | Journal: Science / Year: 2015 Title: TRANSCRIPTION. Allosteric transcriptional regulation via changes in the overall topology of the core promoter. Authors: Philips, S.J. / Canalizo-Hernandez, M. / Yildirim, I. / Schatz, G.C. / Mondragon, A. / O'Halloran, T.V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4wlw.cif.gz | 72.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4wlw.ent.gz | 48.8 KB | Display | PDB format |
PDBx/mmJSON format | 4wlw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wl/4wlw ftp://data.pdbj.org/pub/pdb/validation_reports/wl/4wlw | HTTPS FTP |
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-Related structure data
Related structure data | 4wlsC 1q06S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | THE BIOLOGICAL OLIGOMERIZATION STATE OF CUER IS A DIMER. IN THE STRUCTURE, THE CUER MONOMER IS BOUND TO DNA DUPLEX (CHAINS X AND Y) |
-Components
#1: Protein | Mass: 15396.852 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: cueR, ybbI, b0487, JW0476 / Plasmid: PET24A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A9G4 |
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#2: DNA chain | Mass: 7008.510 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: DNA chain | Mass: 7115.600 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#4: Chemical | ChemComp-AG / |
Sequence details | MICRO-HETEROGENEITY IS OBSERVED. TWO ORIENTATIONS OF THE DNA WERE OBSERVED. THE GIVEN SEQRES ...MICRO-HETEROGENE |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.17 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.1M IMIDAZOLE, PH 8.0, 0.2M CA(C2H3O2)2 AND 8% PEG8000, VAPOR DIFFUSION, HANGING DROP TEMPERATURE 296K PH range: 8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9785 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 22, 2007 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→29.42 Å / Num. obs: 10637 / % possible obs: 99.4 % / Observed criterion σ(I): 4 / Redundancy: 6.6 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 16.4 |
Reflection shell | Resolution: 2.8→2.95 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 3.6 / % possible all: 97.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1Q06 Resolution: 2.8→24.93 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.892 / SU B: 14.231 / SU ML: 0.28 / Cross valid method: THROUGHOUT / ESU R: 0.556 / ESU R Free: 0.332 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.873 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→24.93 Å
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