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- PDB-4u0y: Crystal structure of the DNA-binding domains of YvoA in complex w... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4u0y | |||||||||
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Title | Crystal structure of the DNA-binding domains of YvoA in complex with palindromic operator DNA | |||||||||
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![]() | TRANSCRIPTION / Repressor / Bacterial transcription regulation / Transcription factor / GntR/HutC family / Winged helix-turn-helix motif / N-acetylglucosamine utilization / DNA-binding / Operator-binding | |||||||||
Function / homology | ![]() DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Fillenberg, S.B. / Muller, Y.A. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural insight into operator dre-sites recognition and effector binding in the GntR/HutC transcription regulator NagR. Authors: Fillenberg, S.B. / Grau, F.C. / Seidel, G. / Muller, Y.A. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 98.8 KB | Display | ![]() |
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PDB format | ![]() | 71.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 457.9 KB | Display | ![]() |
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Full document | ![]() | 460.8 KB | Display | |
Data in XML | ![]() | 16.5 KB | Display | |
Data in CIF | ![]() | 24.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4u0vC ![]() 4u0wC ![]() 4wwcC ![]() 2wv0S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 8965.283 Da / Num. of mol.: 4 / Fragment: UNP residues 1-75 Source method: isolated from a genetically manipulated source Details: Truncated form of YvoA; comprises only the DNA-binding domain (residues 1-75) Source: (gene. exp.) ![]() ![]() Gene: yvoA, BSU35030 / Production host: ![]() ![]() #2: DNA chain | Mass: 4584.984 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: 15mer palindromic dsDNA construct; derived from the consensus sequence of the two native non-palindromic dre-site sequences upstream of nagAB-yvoA and nagP Source: (synth.) ![]() ![]() #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.46 % |
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Crystal grow | Temperature: 292.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 50 mM sodium cacodylate, 200 mM sodium citrate, 10 mM MgCl2, 5 % (v/v) isopropanol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Oct 8, 2010 |
Radiation | Monochromator: Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 1.91→32.52 Å / Num. obs: 31230 / % possible obs: 99.8 % / Redundancy: 3.8 % / Biso Wilson estimate: 25.86 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 10.61 |
Reflection shell | Resolution: 1.91→1.98 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.87 / Mean I/σ(I) obs: 1.9 / % possible all: 98.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: DNA-binding domain of PDB entry 2wv0 Resolution: 1.91→32.52 Å / Occupancy max: 1 / Occupancy min: 0.45 / FOM work R set: 0.8245 / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.95 / Phase error: 25.14 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 99.38 Å2 / Biso mean: 29.8537 Å2 / Biso min: 13.23 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.91→32.52 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11
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