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Open data
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Basic information
Entry | Database: PDB / ID: 5f7p | ||||||
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Title | Rok Repressor Lmo0178 from Listeria monocytogenes | ||||||
![]() | Lmo0178 protein | ||||||
![]() | TRANSCRIPTION / Repressor / Open reading frame / Kinase / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID | ||||||
Function / homology | ROK family / ROK family / Winged helix-turn-helix DNA-binding / ATPase, nucleotide binding domain / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / metal ion binding / Lmo0178 protein![]() | ||||||
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 | ![]() | 275 KB | Display | ![]() |
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PDB format | ![]() | 223.2 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 ![]() 5f7qC ![]() 5f7rSC ![]() 5f7sC ![]() 5f7uC ![]() 5f7vC C: citing same article ( S: Starting model for refinement |
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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: 45366.551 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC BAA-679 / EGD-e / Gene: lmo0178 / Production host: ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.91 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, sitting drop Details: 10 mg/mL proten in 10 mM Tris, pH 8.3, 100 mM sodium chloride against JCSG+ (Qiagen) A10 (0.2 M potassium formate, 20% 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: 2.838→70.757 Å / Num. obs: 19017 / % possible obs: 97.7 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.033 / Net I/σ(I): 27.1 |
Reflection shell | Resolution: 2.838→2.9 Å / Redundancy: 5 % / Rmerge(I) obs: 0.628 / Mean I/σ(I) obs: 2.3 / % possible all: 98.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 5F7R Resolution: 2.84→70.757 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.899 / SU B: 42.326 / SU ML: 0.384 / Cross valid method: THROUGHOUT / ESU R Free: 0.455 / 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: 103.604 Å2
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Refinement step | Cycle: LAST / Resolution: 2.84→70.757 Å
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