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Yorodumi- PDB-4wxe: CRYSTAL STRUCTURE OF A LACI REGULATOR FROM LACTOBACILLUS CASEI (L... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4wxe | ||||||
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Title | CRYSTAL STRUCTURE OF A LACI REGULATOR FROM LACTOBACILLUS CASEI (LSEI_2103, TARGET EFI-512911) WITH BOUND TRIS | ||||||
Components | Transcriptional regulator, LacI familyTranscriptional regulation | ||||||
Keywords | TRANSCRIPTION / LACI REGULATOR / ENZYME FUNCTION INITIATIVE / EFI / Structural Genomics | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Lactobacillus casei (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å | ||||||
Authors | Vetting, M.W. / Al Obaidi, N.F. / Toro, R. / Morisco, L.L. / Benach, J. / Wasserman, S.R. / Attonito, J.D. / Scott Glenn, A. / Chamala, S. / Chowdhury, S. ...Vetting, M.W. / Al Obaidi, N.F. / Toro, R. / Morisco, L.L. / Benach, J. / Wasserman, S.R. / Attonito, J.D. / Scott Glenn, A. / Chamala, S. / Chowdhury, S. / Lafleur, J. / Love, J. / Seidel, R.D. / Whalen, K.L. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI) | ||||||
Citation | Journal: To be published Title: CRYSTAL STRUCTURE OF A LACI REGULATOR FROM LACTOBACILLUS CASEI (LSEI_2103, TARGET EFI-512911) WITH BOUND TRIS Authors: Vetting, M.W. / Al Obaidi, N.F. / Toro, R. / Morisco, L.L. / Benach, J. / Wasserman, S.R. / Attonito, J.D. / Scott Glenn, A. / Chamala, S. / Chowdhury, S. / Lafleur, J. / Love, J. / Seidel, ...Authors: Vetting, M.W. / Al Obaidi, N.F. / Toro, R. / Morisco, L.L. / Benach, J. / Wasserman, S.R. / Attonito, J.D. / Scott Glenn, A. / Chamala, S. / Chowdhury, S. / Lafleur, J. / Love, J. / Seidel, R.D. / Whalen, K.L. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4wxe.cif.gz | 173.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4wxe.ent.gz | 147.6 KB | Display | PDB format |
PDBx/mmJSON format | 4wxe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wx/4wxe ftp://data.pdbj.org/pub/pdb/validation_reports/wx/4wxe | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-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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Details | biological unit is a dimer |
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 33302.539 Da / Num. of mol.: 1 / Fragment: UNP residues 54-333 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactobacillus casei (bacteria) / Strain: ATCC 334 / Gene: LSEI_2103 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q036L9 |
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-Non-polymers , 5 types, 417 molecules
#2: Chemical | ChemComp-TRS / | ||||||
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#3: Chemical | #4: Chemical | ChemComp-EDO / | #5: Chemical | ChemComp-MG / | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 39.96 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: Protein (30.7 mg/ml, 10 mM HEPES pH 7.5, 5 mM DTT); Reservoir ((MCSG4 F4), 0.2 M Magnesium Chloride, 0.1 M Tris pH 8.5, 16%(w/v) PEG 4000, 0.2M Lithium Chloride, 20 %(w/v) PEG 3350); ...Details: Protein (30.7 mg/ml, 10 mM HEPES pH 7.5, 5 mM DTT); Reservoir ((MCSG4 F4), 0.2 M Magnesium Chloride, 0.1 M Tris pH 8.5, 16%(w/v) PEG 4000, 0.2M Lithium Chloride, 20 %(w/v) PEG 3350); Cryoprotection (80% Reservoir + 20% Ethylene Glycol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Aug 12, 2014 / Details: MIRRORS |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→25.473 Å / Num. obs: 43692 / % possible obs: 100 % / Redundancy: 22.1 % / Biso Wilson estimate: 12.77 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.027 / Net I/σ(I): 21.5 / Num. measured all: 964401 / Scaling rejects: 79 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 21.9 % / Rmerge(I) obs: 0.952 / Mean I/σ(I) obs: 4.2 / Num. measured all: 46843 / Num. unique all: 2142 / CC1/2: 0.91 / Rpim(I) all: 0.207 / Rejects: 0 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.5→25.473 Å / FOM work R set: 0.9109 / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.53 / 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: 65.47 Å2 / Biso mean: 17.81 Å2 / Biso min: 5.43 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.5→25.473 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: 16 / % reflection obs: 100 %
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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