+Open data
-Basic information
Entry | Database: PDB / ID: 4p7d | ||||||
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Title | Antitoxin HicB3 crystal structure | ||||||
Components | Antitoxin HicB3 | ||||||
Keywords | TOXIN / toxin-antitoxin complex / homotetramer | ||||||
Function / homology | Function and homology information sequence-specific DNA binding / regulation of DNA-templated transcription Similarity search - Function | ||||||
Biological species | Yersinia pestis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.781 Å | ||||||
Authors | Li de la Sierra-Gallay, I. / Bibi-Triki, S. / van Tilbeurgh, H. / Lazar, N. / Pradel, E. | ||||||
Citation | Journal: J.Bacteriol. / Year: 2014 Title: Functional and Structural Analysis of HicA3-HicB3, a Novel Toxin-Antitoxin System of Yersinia pestis. Authors: Bibi-Triki, S. / Li de la Sierra-Gallay, I. / Lazar, N. / Leroy, A. / Van Tilbeurgh, H. / Sebbane, F. / Pradel, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4p7d.cif.gz | 113.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4p7d.ent.gz | 94.6 KB | Display | PDB format |
PDBx/mmJSON format | 4p7d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p7/4p7d ftp://data.pdbj.org/pub/pdb/validation_reports/p7/4p7d | HTTPS FTP |
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-Related 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: 16475.211 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Yersinia pestis (bacteria) / Gene: YPO3369 / Production host: Escherichia coli (E. coli) / References: UniProt: Q0WBS6, UniProt: A0A5P8YCM0*PLUS #2: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 48.89 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: polyethylene glycol 3000, MES pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97911 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 5, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97911 Å / Relative weight: 1 |
Reflection | Resolution: 2.78→46.85 Å / Num. obs: 16491 / % possible obs: 99.5 % / Redundancy: 7.1 % / Biso Wilson estimate: 69.76 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 14.45 |
Reflection shell | Resolution: 2.78→2.95 Å / Redundancy: 7 % / Rmerge(I) obs: 0.683 / Mean I/σ(I) obs: 2.84 / % possible all: 97.2 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.781→46.846 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.39 / 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 mean: 63.42 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.781→46.846 Å
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Refine LS restraints |
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LS refinement shell |
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