+Open data
-Basic information
Entry | Database: PDB / ID: 6lty | ||||||
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Title | DNA bound antitoxin HigA3 | ||||||
Components |
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Keywords | ANTITOXIN / DNA BINDING PROTEIN/DNA / DNA BINDING PROTEIN-DNA COMPLEX | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Mycobacterium tuberculosis H37Rv (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.28 Å | ||||||
Authors | Park, J.Y. / Lee, B.J. | ||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: Iucrj / Year: 2020 Title: Induced DNA bending by unique dimerization of HigA antitoxin. Authors: Park, J.Y. / Kim, H.J. / Pathak, C. / Yoon, H.J. / Kim, D.H. / Park, S.J. / Lee, B.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6lty.cif.gz | 67.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6lty.ent.gz | 45.6 KB | Display | PDB format |
PDBx/mmJSON format | 6lty.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lt/6lty ftp://data.pdbj.org/pub/pdb/validation_reports/lt/6lty | HTTPS FTP |
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-Related structure data
Related structure data | 6ltzSC S: Starting model for refinement C: citing same article (ref.) |
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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: 12891.620 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria) Strain: H37Rv / Gene: higA3, Rv3183 / Production host: Escherichia coli (E. coli) / References: UniProt: O53333 #2: DNA chain | | Mass: 6136.008 Da / Num. of mol.: 1 / Source method: obtained synthetically Source: (synth.) Mycobacterium tuberculosis H37Rv (bacteria) #3: DNA chain | | Mass: 6130.961 Da / Num. of mol.: 1 / Source method: obtained synthetically Source: (synth.) Mycobacterium tuberculosis H37Rv (bacteria) |
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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: 2.9 Å3/Da / Density % sol: 57.53 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 23% w/v PEG3350, 0.2 M sodium acetate trihydrate pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9796 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 21, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9796 Å / Relative weight: 1 |
Reflection | Resolution: 3.277→50 Å / Num. obs: 6656 / % possible obs: 99.3 % / Redundancy: 2.6 % / Rrim(I) all: 0.072 / Net I/σ(I): 27.3 |
Reflection shell | Resolution: 3.277→3.36 Å / Num. unique obs: 316 / Rrim(I) all: 0.654 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6LTZ Resolution: 3.28→41.79 Å / Cor.coef. Fo:Fc: 0.841 / Cor.coef. Fo:Fc free: 0.88 / SU B: 29.198 / SU ML: 0.54 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 284.12 Å2 / Biso mean: 142.107 Å2 / Biso min: 77.14 Å2
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Refinement step | Cycle: final / Resolution: 3.28→41.79 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.28→3.362 Å / Rfactor Rfree error: 0
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