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Yorodumi- PDB-4rk1: Crystal structure of LacI family transcriptional regulator from E... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4rk1 | |||||||||
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Title | Crystal structure of LacI family transcriptional regulator from Enterococcus faecium, Target EFI-512930, with bound ribose | |||||||||
Components | Ribose transcriptional regulator | |||||||||
Keywords | TRANSCRIPTION REGULATOR / sugar binding / transcription regulation / Enzyme Function Initiative / EFI / structural genomics / transcriptional factor / D-glucose | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Enterococcus faecium DO (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å | |||||||||
Authors | 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) | |||||||||
Citation | Journal: To be Published Title: Crystal Structure of LacI Transcriptional Regulator Rbsr from Enterococcus faecium, Target EFI-512930 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4rk1.cif.gz | 345 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4rk1.ent.gz | 286.6 KB | Display | PDB format |
PDBx/mmJSON format | 4rk1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4rk1_validation.pdf.gz | 479.3 KB | Display | wwPDB validaton report |
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Full document | 4rk1_full_validation.pdf.gz | 489.4 KB | Display | |
Data in XML | 4rk1_validation.xml.gz | 69.4 KB | Display | |
Data in CIF | 4rk1_validation.cif.gz | 99.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rk/4rk1 ftp://data.pdbj.org/pub/pdb/validation_reports/rk/4rk1 | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper:
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-Components
#1: Protein | Mass: 31689.443 Da / Num. of mol.: 6 / Fragment: UNP residues 61-339 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterococcus faecium DO (bacteria) / Gene: rbsR, HMPREF0351_10453 / Plasmid: pET / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: I3TZ89 #2: Sugar | ChemComp-RIB / #3: Chemical | ChemComp-CL / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.33 Å3/Da / Density % sol: 63.01 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: protein in 10 mM Bis-Tris, 500 mM sodium chloride, 10% glycerol, 5 mM DTT, TEV protease (1:100 ratio), reservoir: 1 M sodium acetate:HCl, pH 4.6, 1.5 M ammonium chloride, 10 mM D-glucose, ...Details: protein in 10 mM Bis-Tris, 500 mM sodium chloride, 10% glycerol, 5 mM DTT, TEV protease (1:100 ratio), reservoir: 1 M sodium acetate:HCl, pH 4.6, 1.5 M ammonium chloride, 10 mM D-glucose, cryoprotectant = reservoir + 30% w/v glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 5, 2014 / Details: mirrors |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 197594 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 5.2 % / Rmerge(I) obs: 0.1 / Rsym value: 0.1 / Net I/σ(I): 16.9 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.93 / Mean I/σ(I) obs: 1.8 / Rsym value: 0.93 / % possible all: 95.7 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.814 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.101 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.347 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→50 Å
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Refine LS restraints |
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