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- PDB-5f7q: ROK repressor Lmo0178 from Listeria monocytogenes bound to operator -
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Open data
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Basic information
Entry | Database: PDB / ID: 5f7q | ||||||
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Title | ROK repressor Lmo0178 from Listeria monocytogenes bound to operator | ||||||
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![]() | TRANSCRIPTION/DNA / repressor / open reading frame / kinase / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / TRANSCRIPTION-DNA complex | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Light, S.H. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
![]() | ![]() Title: Structure to function of an alpha-glucan metabolic pathway that promotes Listeria monocytogenes pathogenesis. Authors: Light, S.H. / Cahoon, L.A. / Halavaty, A.S. / Freitag, N.E. / Anderson, W.F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 701.1 KB | Display | ![]() |
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PDB format | ![]() | 578.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4kmqC ![]() 5do8C ![]() 5f7pC ![]() 5f7rSC ![]() 5f7sC ![]() 5f7uC ![]() 5f7vC 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
-Protein , 1 types, 4 molecules CEJL
#1: Protein | Mass: 45366.551 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC BAA-679 / EGD-e / Gene: lmo0178 / Production host: ![]() ![]() |
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-DNA chain , 2 types, 2 molecules FK
#2: DNA chain | Mass: 9533.195 Da / Num. of mol.: 1 / Source method: obtained synthetically Source: (synth.) ![]() |
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#3: DNA chain | Mass: 9524.181 Da / Num. of mol.: 1 / Source method: obtained synthetically Source: (synth.) ![]() |
-Non-polymers , 6 types, 291 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/PG5.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/7PE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PG5.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/7PE.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-ZN / #5: Chemical | #6: Chemical | #7: Chemical | ChemComp-PEG / #8: Chemical | #9: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.69 Å3/Da / Density % sol: 54.23 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, sitting drop Details: 7.5 mg/mL protein in 0.5 M sodium chloride, 0.01 M Tris-HCl, pH 8.3 against Classics II H6 (Qiagen, 0.2 M sodium formate, 20% w/v PEG3350) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 20, 2015 |
Radiation | Monochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→30 Å / Num. obs: 81757 / % possible obs: 100 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 28.7 |
Reflection shell | Resolution: 2.4→2.44 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.71 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5F7R Resolution: 2.4→30 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.946 / SU B: 14.68 / SU ML: 0.169 / Cross valid method: THROUGHOUT / ESU R: 0.364 / ESU R Free: 0.227 / 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: 58.79 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→30 Å
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Refine LS restraints |
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