+Open data
-Basic information
Entry | Database: PDB / ID: 4kt5 | ||||||
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Title | Structure of GrlR-GrlA complex | ||||||
Components |
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Keywords | TRANSCRIPTION REGULATOR / Beta Barrel / HTH motif / Regulator | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å | ||||||
Authors | Padavannil, A. / Jobichen, C. / Sivaraman, J. | ||||||
Citation | Journal: Nat Commun / Year: 2013 Title: Structure of GrlR-GrlA complex that prevents GrlA activation of virulence genes Authors: Padavannil, A. / Jobichen, C. / Mills, E. / Velazquez-Campoy, A. / Li, M. / Leung, K.Y. / Mok, Y.K. / Rosenshine, I. / Sivaraman, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4kt5.cif.gz | 140.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4kt5.ent.gz | 116.5 KB | Display | PDB format |
PDBx/mmJSON format | 4kt5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4kt5_validation.pdf.gz | 453.3 KB | Display | wwPDB validaton report |
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Full document | 4kt5_full_validation.pdf.gz | 457.6 KB | Display | |
Data in XML | 4kt5_validation.xml.gz | 14 KB | Display | |
Data in CIF | 4kt5_validation.cif.gz | 17.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kt/4kt5 ftp://data.pdbj.org/pub/pdb/validation_reports/kt/4kt5 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 14430.923 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: O157:H7 / Gene: grlR / Plasmid: pET-DUET1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: Q7DB61 #2: Protein | | Mass: 16250.247 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: O157:H7 / Gene: grlA / Plasmid: pET-DUET1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: Q7DB62 #3: Chemical | #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: 2.38 Å3/Da / Density % sol: 48.21 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 Details: PEG 3350, 0.1M Sodium Malonate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.9795 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 11, 2011 / Details: Mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. all: 22108 / Num. obs: 22108 / % possible obs: 97.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 49.55 Å2 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.7→14.915 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.38 / σ(F): 1.35 / Phase error: 28.65 / Stereochemistry target values: ML Details: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS IN THE STRUCTURE FACTOR DATA
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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: 148.32 Å2 / Biso mean: 57.3101 Å2 / Biso min: 23.73 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→14.915 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
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Refinement TLS params. | Method: refined / Origin x: -21.4218 Å / Origin y: 27.1768 Å / Origin z: -17.4445 Å
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Refinement TLS group | Selection details: ALL |