+Open data
-Basic information
Entry | Database: PDB / ID: 2h1o | ||||||
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Title | Structure of FitAB bound to IR36 DNA fragment | ||||||
Components |
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Keywords | GENE REGULATION/DNA COMPLEX / PIN domain / RHH protein / DNA binding / tetramer of dimers / GENE REGULATION-DNA COMPLEX COMPLEX | ||||||
Function / homology | Function and homology information migration in host / RNA nuclease activity / sequence-specific DNA binding / Hydrolases; Acting on ester bonds / regulation of DNA-templated transcription / magnesium ion binding / protein homodimerization activity / DNA binding Similarity search - Function | ||||||
Biological species | Neisseria gonorrhoeae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Mattison, K. / Wilbur, J.S. / So, M. / Brennan, R.G. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2006 Title: Structure of FitAB from Neisseria gonorrhoeae bound to DNA reveals a tetramer of toxin-antitoxin heterodimers containing pin domains and ribbon-helix-helix motifs. Authors: Mattison, K. / Wilbur, J.S. / So, M. / Brennan, R.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2h1o.cif.gz | 208 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2h1o.ent.gz | 161.7 KB | Display | PDB format |
PDBx/mmJSON format | 2h1o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h1/2h1o ftp://data.pdbj.org/pub/pdb/validation_reports/h1/2h1o | HTTPS FTP |
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-Related structure data
Related structure data | 2bsqC 2h1cSC 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: DNA chain | Mass: 11169.996 Da / Num. of mol.: 1 / Mutation: iodo / Source method: obtained synthetically / Details: sequence upstream of FitAB promoter region | ||||
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#2: DNA chain | Mass: 11198.117 Da / Num. of mol.: 1 / Mutation: iodo / Source method: obtained synthetically / Details: sequence upstream of FitAB promoter region | ||||
#3: Protein | Mass: 15919.320 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neisseria gonorrhoeae (bacteria) / Gene: fitB / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): bl21 / References: UniProt: Q9RF91, UniProt: Q5F882*PLUS #4: Protein | Mass: 7283.293 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neisseria gonorrhoeae (bacteria) / Gene: fitA / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): bl21 / References: UniProt: Q9RF92, UniProt: Q5F881*PLUS #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.61 Å3/Da / Density % sol: 65.94 % | ||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 0.1 M sodium acetate, pH 4.0, 0.27 M sodium acetate, pH 7.0, 7.2 % PEG 20,000, 7.2 % PEG monomethyl ether 550, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.0332 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 8, 2005 |
Radiation | Monochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 2.99→70.36 Å / Num. all: 33360 / Num. obs: 33243 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1.5 / Rsym value: 0.178 / Net I/σ(I): 3.1 |
Reflection shell | Resolution: 2.99→3.14 Å / Mean I/σ(I) obs: 44 / Rsym value: 0.015 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2H1C Resolution: 3→70.36 Å / Rfactor Rfree error: 0.005 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: CNS bulk solvent model used / Bsol: 25.6821 Å2 / ksol: 0.316642 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.87 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3→70.36 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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