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Yorodumi- PDB-3s8q: Crystal structure of the R-M controller protein C.Esp1396I OL ope... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3s8q | ||||||
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Title | Crystal structure of the R-M controller protein C.Esp1396I OL operator complex | ||||||
Components |
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Keywords | Protein binding/DNA / Protein-DNA complex / Helix-turn-helix / Transcriptional Regulator / DNA-binding protein / Protein binding-DNA complex | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Enterobacter sp. RFL1396 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å | ||||||
Authors | McGeehan, J.E. / Ball, N.J. / Streeter, S.D. / Thresh, S.-J. / Kneale, G.G. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2012 Title: Recognition of dual symmetry by the controller protein C.Esp1396I based on the structure of the transcriptional activation complex. Authors: McGeehan, J.E. / Ball, N.J. / Streeter, S.D. / Thresh, S.J. / Kneale, G.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3s8q.cif.gz | 125.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3s8q.ent.gz | 95.4 KB | Display | PDB format |
PDBx/mmJSON format | 3s8q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3s8q_validation.pdf.gz | 441.3 KB | Display | wwPDB validaton report |
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Full document | 3s8q_full_validation.pdf.gz | 453.1 KB | Display | |
Data in XML | 3s8q_validation.xml.gz | 14.2 KB | Display | |
Data in CIF | 3s8q_validation.cif.gz | 21 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s8/3s8q ftp://data.pdbj.org/pub/pdb/validation_reports/s8/3s8q | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 9521.175 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacter sp. RFL1396 (bacteria) / Gene: esp1396IC / Plasmid: pET23 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Gold / References: UniProt: Q8GGH0 #2: DNA chain | | Mass: 5850.794 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: C.Esp1396I #3: DNA chain | | Mass: 5797.788 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA #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: 2.53 Å3/Da / Density % sol: 51.3 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.2 M Sodium acetate, 0.1 m Bis-tris-propane, 20% w/v PEG 3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 30, 2008 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9334 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.1→50 Å / Num. all: 17823 / Num. obs: 17823 / % possible obs: 94.6 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Biso Wilson estimate: 31.238 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 14.66 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.936 / WRfactor Rfree: 0.2025 / WRfactor Rwork: 0.15 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8634 / SU B: 10.058 / SU ML: 0.116 / SU R Cruickshank DPI: 0.1917 / SU Rfree: 0.1776 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.178 / 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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 206.61 Å2 / Biso mean: 32.61 Å2 / Biso min: 12.87 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.154 Å / Total num. of bins used: 20
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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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