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Open data
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Basic information
Entry | Database: PDB / ID: 1xsd | ||||||
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Title | Crystal structure of the BlaI repressor in complex with DNA | ||||||
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![]() | TRANSCRIPTION/DNA / ![]() | ||||||
Function / homology | ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Safo, M.K. / Ko, T.-P. / Musayev, F.N. / Zhao, Q. / Robinson, H. / Scarsdale, N. / Wang, A.H.-J. / Archer, G.L. | ||||||
![]() | ![]() Title: Crystal structures of the BlaI repressor from Staphylococcus aureus and its complex with DNA: insights into transcriptional regulation of the bla and mec operons Authors: Safo, M.K. / Zhao, Q. / Ko, T.-P. / Musayev, F.N. / Robinson, H. / Scarsdale, N. / Wang, A.H.-J. / Archer, G.L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 56.1 KB | Display | ![]() |
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PDB format | ![]() | 37.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1sd4C ![]() 1sd6C ![]() 1sd7C ![]() 1okrS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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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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Details | the second part of the dimer is generated by the two-fold symmetry operator of (-x, -y, z) |
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Components
#1: DNA chain | Mass: 4896.216 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: Protein | Mass: 14988.363 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() |
#3: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.3 Å3/Da / Density % sol: 71.5 % |
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Crystal grow![]() | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG 8000, ethylene glycol, magnesium chloride, sodium HEPES, potasssium phosphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Feb 5, 2004 |
Radiation | Monochromator: CHANNEL-CUT SI CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.7→30 Å / Num. all: 9291 / Num. obs: 9285 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.7 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 44 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 11.8 % / Rmerge(I) obs: 0.546 / Mean I/σ(I) obs: 4.5 / Num. unique all: 901 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB entry 1OKR Resolution: 2.7→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: The 16 nucleotide DNA model in this structure represents an average of the 32 base-pair DNA used in crystallization. (Used the 32 base-pair DNA of 5'-GACTACATTTGTAGTATATTACAAATGTAGTA-3' and ...Details: The 16 nucleotide DNA model in this structure represents an average of the 32 base-pair DNA used in crystallization. (Used the 32 base-pair DNA of 5'-GACTACATTTGTAGTATATTACAAATGTAGTA-3' and 5'-TACTACATTTGTAATATACTACAAATGTAGTC-3') It contains phosphate groups at both 5' and 3' ends. There are a number of wide solvent channels in this crystal. In the void volume between the protein-DNA complex molecules some spiral densities are modeled as strings of water molecules. These are possibly a result of residuals of the averaged model of the DNA. It is also possible that this void volume may host some DNA molecules with low occupancies.
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.8 Å
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