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- PDB-4rk4: Crystal structure of LacI family transcriptional regulator from L... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4rk4 | ||||||
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Title | Crystal structure of LacI family transcriptional regulator from Lactobacillus casei, Target EFI-512911, with bound glucose | ||||||
![]() | Transcriptional regulator, LacI family | ||||||
![]() | TRANSCRIPTION REGULATOR / sugar binding / transcription regulation / Enzyme Function Initiative / EFI / structural genomics / transcriptional factor / D-glucose | ||||||
Function / homology | ![]() transcription cis-regulatory region binding / DNA-binding transcription factor activity Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Patskovsky, Y. / Toro, R. / Bhosle, R. / Al Obaidi, N. / Chamala, S. / Attonito, J.D. / Scott Glenn, A. / Chowdhury, S. / Lafleur, J. / Siedel, R.D. ...Patskovsky, Y. / Toro, R. / Bhosle, R. / Al Obaidi, N. / Chamala, S. / Attonito, J.D. / Scott Glenn, A. / Chowdhury, S. / Lafleur, J. / Siedel, R.D. / Hillerich, B. / Love, J. / Whalen, K.L. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI) | ||||||
![]() | ![]() Title: Crystal Structure of LacI Transcriptional Regulator Lsei_2103 from Lactobacillus casei, Target EFI-512911 Authors: Patskovsky, Y. / Toro, R. / Bhosle, R. / Al Obaidi, N. / Chamala, S. / Scott Glenn, A. / Attonito, J.D. / Chowdhury, S. / Lafleur, J. / Siedel, R.D. / Hillerich, B. / Love, J. / Whalen, K.L. ...Authors: Patskovsky, Y. / Toro, R. / Bhosle, R. / Al Obaidi, N. / Chamala, S. / Scott Glenn, A. / Attonito, J.D. / Chowdhury, S. / Lafleur, J. / Siedel, R.D. / Hillerich, B. / Love, J. / Whalen, K.L. / Gerlt, J.A. / Almo, S.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 131.4 KB | Display | ![]() |
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PDB format | ![]() | 102 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 441.1 KB | Display | ![]() |
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Full document | ![]() | 442.5 KB | Display | |
Data in XML | ![]() | 14.9 KB | Display | |
Data in CIF | ![]() | 22.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4rk5C ![]() 3rk3S C: citing same article ( S: Starting model for refinement |
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Similar structure data | |
Other databases |
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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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Components
#1: Protein | Mass: 30630.756 Da / Num. of mol.: 1 / Fragment: UNP residues 54-333 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: LSEI_2103 / Plasmid: pET / Production host: ![]() ![]() |
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#2: Sugar | ChemComp-GLC / |
#3: Chemical | ChemComp-NA / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.5 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: protein in 10 mM Bis-Tris, 500 mM sodium chloride, 10% glycerol, 5 mM DTT, TEV protease (1:100 ratio), reservoir: 0.16 M calcium acetate, 0.08 M sodium cacodylate, pH 6.5, 14.4% PEG8000, 20% ...Details: protein in 10 mM Bis-Tris, 500 mM sodium chloride, 10% glycerol, 5 mM DTT, TEV protease (1:100 ratio), reservoir: 0.16 M calcium acetate, 0.08 M sodium cacodylate, pH 6.5, 14.4% PEG8000, 20% glycerol, cryoprotectant = reservoir + 100 mM glucose, VAPOR DIFFUSION, SITTING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 25, 2014 / Details: mirrors |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 |
Reflection | Resolution: 1.32→50 Å / Num. obs: 67029 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 8.9 % / Rmerge(I) obs: 0.041 / Rsym value: 0.041 / Net I/σ(I): 40.1 |
Reflection shell | Resolution: 1.32→1.34 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.94 / Mean I/σ(I) obs: 2 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3RK3 Resolution: 1.32→50 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.975 / SU B: 1.303 / SU ML: 0.024 / Cross valid method: THROUGHOUT / ESU R: 0.039 / ESU R Free: 0.039 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. SIDE CHAIN ATOMS (CG, CD1, CD2, CE1, CE2, CZ) OF RESIDUE A PHE 281 ARE ON A SPECIAL POSITION.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.285 Å2
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Refinement step | Cycle: LAST / Resolution: 1.32→50 Å
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Refine LS restraints |
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