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Yorodumi- PDB-7kci: DETERMINANTS OF REPRESSOR/OPERATOR RECOGNITION FROM THE STRUCTURE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7kci | ||||||||||||
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Title | DETERMINANTS OF REPRESSOR/OPERATOR RECOGNITION FROM THE STRUCTURE OF THE TRP OPERATOR BINDING SITE | ||||||||||||
Components | Self-complementary deoxyoligonucleotide decamer d(CCACTAGTGG) | ||||||||||||
Keywords | DNA / B-DNA / DOUBLE HELIX / DEOXYRIBONUCLEIC ACID | ||||||||||||
Function / homology | DNA Function and homology information | ||||||||||||
Biological species | synthetic construct (others) | ||||||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||||||||
Authors | Shakked, Z. / Guzikevich-Guerstein, G. / Frolow, F. / Rabinovich, D. / Joachimiak, A. / Sigler, P.B. | ||||||||||||
Funding support | 3items
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Citation | Journal: Nature / Year: 1994 Title: Determinants of repressor/operator recognition from the structure of the trp operator binding site. Authors: Shakked, Z. / Guzikevich-Guerstein, G. / Frolow, F. / Rabinovich, D. / Joachimiak, A. / Sigler, P.B. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7kci.cif.gz | 27.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7kci.ent.gz | 15.5 KB | Display | PDB format |
PDBx/mmJSON format | 7kci.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7kci_validation.pdf.gz | 323.6 KB | Display | wwPDB validaton report |
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Full document | 7kci_full_validation.pdf.gz | 347.8 KB | Display | |
Data in XML | 7kci_validation.xml.gz | 4.4 KB | Display | |
Data in CIF | 7kci_validation.cif.gz | 6.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kc/7kci ftp://data.pdbj.org/pub/pdb/validation_reports/kc/7kci | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: DNA chain | Mass: 3045.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #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: 2.44 Å3/Da / Density % sol: 49.58 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 7 / Details: PEG 200, NA CACODYLATE, SPERMINE_HCL, MGCL2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å |
Detector | Type: RIGAKU AFC-5R / Detector: DIFFRACTOMETER |
Radiation | Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→33 Å / Num. obs: 4034 / Redundancy: 2.03 % / Rsym value: 0.087 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: standard B-DNA model Resolution: 1.95→6 Å / Cross valid method: THROUGHOUT / σ(F): 2 /
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Displacement parameters | Biso max: 100.9 Å2 / Biso mean: 16.9851 Å2 / Biso min: 2 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→6 Å
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