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Yorodumi- PDB-1owf: Crystal structure of a mutant IHF (BetaE44A) complexed with the n... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1owf | ||||||
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Title | Crystal structure of a mutant IHF (BetaE44A) complexed with the native H' Site | ||||||
Components |
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Keywords | TRANSCRIPTION/DNA / protein-DNA recognition / indirect readout / IHF / DNA bending / minor groove / TRANSCRIPTION-DNA COMPLEX | ||||||
Function / homology | Function and homology information IHF-DNA complex / DNA-binding transcription activator activity / protein-DNA complex / structural constituent of chromatin / regulation of translation / chromosome / DNA recombination / transcription cis-regulatory region binding / DNA-templated transcription / regulation of DNA-templated transcription ...IHF-DNA complex / DNA-binding transcription activator activity / protein-DNA complex / structural constituent of chromatin / regulation of translation / chromosome / DNA recombination / transcription cis-regulatory region binding / DNA-templated transcription / regulation of DNA-templated transcription / DNA binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.95 Å | ||||||
Authors | Lynch, T.W. / Read, E.K. / Mattis, A.N. / Gardner, J.F. / Rice, P.A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2003 Title: Integration Host Factor: putting a twist on protein-DNA recognition Authors: Lynch, T.W. / Read, E.K. / Mattis, A.N. / Gardner, J.F. / Rice, P.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1owf.cif.gz | 92.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1owf.ent.gz | 66.7 KB | Display | PDB format |
PDBx/mmJSON format | 1owf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ow/1owf ftp://data.pdbj.org/pub/pdb/validation_reports/ow/1owf | 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
-DNA chain , 3 types, 3 molecules CDE
#1: DNA chain | Mass: 10801.969 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: DNA chain | Mass: 4611.039 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: DNA chain | Mass: 6074.938 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-Integration Host Factor ... , 2 types, 2 molecules AB
#4: Protein | Mass: 11373.952 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P0A6X7 |
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#5: Protein | Mass: 10613.142 Da / Num. of mol.: 1 / Mutation: E44A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P0A6Y1 |
-Non-polymers , 1 types, 153 molecules
#6: 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: 2.81 Å3/Da / Density % sol: 56.24 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG5000-MME, glycerol, Tris-HCl, magnesium chloride, sodium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 19 ℃ / pH: 7 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9 Å |
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Mar 27, 2002 |
Radiation | Monochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→100 Å / Num. obs: 26109 / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 7 Å2 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.95→42.78 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1278009.76 / Data cutoff high rms absF: 1278009.76 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 44.9462 Å2 / ksol: 0.340265 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.95→42.78 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2.07 Å / Rfactor Rfree error: 0.052 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS % reflection Rfree: 5 % / Rfactor Rfree: 0.275 / Rfactor Rwork: 0.236 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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