+Open data
-Basic information
Entry | Database: PDB / ID: 6ltz | ||||||
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Title | Induced DNA bending by unique dimerization of HigA antitoxin | ||||||
Components | Putative antitoxin HigA3 | ||||||
Keywords | ANTITOXIN | ||||||
Function / homology | HigA2-like, helix-turn-helix domain / Helix-turn-helix domain / Helix-turn-helix XRE-family like proteins / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain / Lambda repressor-like, DNA-binding domain superfamily / DNA binding / DI(HYDROXYETHYL)ETHER / Putative antitoxin HigA3 Function and homology information | ||||||
Biological species | Mycobacterium tuberculosis H37Rv (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.973 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 | 6ltz.cif.gz | 46.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ltz.ent.gz | 30.9 KB | Display | PDB format |
PDBx/mmJSON format | 6ltz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lt/6ltz ftp://data.pdbj.org/pub/pdb/validation_reports/lt/6ltz | 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: 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: Chemical | #3: Chemical | ChemComp-EPE / | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.2 Å3/Da / Density % sol: 44.21 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 1 M ammonium sulfate, 0.1 M HEPES, 0.5% w/v PEG8000 |
-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: 0.9794 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 12, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 1.97→50 Å / Num. obs: 15201 / % possible obs: 100 % / Redundancy: 3.5 % / Rrim(I) all: 0.06 / Net I/σ(I): 41.5 |
Reflection shell | Resolution: 1.97→2 Å / Num. unique obs: 762 / CC1/2: 0.978 / Rrim(I) all: 0.194 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.973→32.113 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.43 / Phase error: 23.06
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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: 110.71 Å2 / Biso mean: 39.4561 Å2 / Biso min: 16.36 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.973→32.113 Å
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LS refinement shell |
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