[English] 日本語
Yorodumi- PDB-2iif: single chain Integration Host Factor mutant protein (scIHF2-K45aE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2iif | ||||||
---|---|---|---|---|---|---|---|
Title | single chain Integration Host Factor mutant protein (scIHF2-K45aE) in complex with DNA | ||||||
Components |
| ||||||
Keywords | RECOMBINATION/DNA / DNA Kinking / bending / U-turn / intercalation / divalent / RECOMBINATION-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) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.72 Å | ||||||
Authors | Bao, Q. / Droege, P. / Davey, C.A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 Title: A Divalent Metal-mediated Switch Controlling Protein-induced DNA Bending Authors: Bao, Q. / Chen, H. / Liu, Y. / Yan, J. / Droge, P. / Davey, C.A. #1: Journal: Nucleic Acids Res. / Year: 2003 Title: Activation of site-specific DNA integration in human cells by a single chain integration host factor Authors: Corona, T. / Bao, Q. / Christ, N. / Schwartz, T. / Li, J. / Droege, P. #2: Journal: Gene / Year: 2004 Title: Single-chain integration host factors as probes for high-precision nucleoprotein complex formation Authors: Bao, Q. / Christ, N. / Droege, P. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2iif.cif.gz | 98.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2iif.ent.gz | 69.9 KB | Display | PDB format |
PDBx/mmJSON format | 2iif.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ii/2iif ftp://data.pdbj.org/pub/pdb/validation_reports/ii/2iif | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-DNA chain , 3 types, 3 molecules CDE
#1: DNA chain | Mass: 10801.969 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: chemically synthesized / Source: (synth.) synthetic construct (others) |
---|---|
#2: DNA chain | Mass: 4611.039 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: chemically synthesized / Source: (synth.) synthetic construct (others) |
#3: DNA chain | Mass: 6074.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: chemically synthesized / Source: (synth.) synthetic construct (others) |
-Protein , 1 types, 1 molecules A
#4: Protein | Mass: 22884.816 Da / Num. of mol.: 1 / Mutation: K89E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P0A6X7, UniProt: P0A6Y1 |
---|
-Non-polymers , 2 types, 171 molecules
#5: Chemical | ChemComp-MN / #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.28 % | ||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1:1 mix water/ well solution containing: 50mM Tris(pH 7.5), 25% PEG5000-MME, 20% glycerol, 50mM NaCl, 7.5mM MnCl2, VAPOR DIFFUSION, HANGING DROP, temperature 291K | ||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
|
-Data collection
Diffraction | Mean temperature: 103 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.542 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 1, 2005 |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.542 Å / Relative weight: 1 |
Reflection | Resolution: 2.72→45 Å / Num. all: 12904 / Num. obs: 12530 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2.72→2.87 Å / % possible all: 95.9 |
-Processing
Software |
| ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 2.72→40 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||
Solvent computation | Bsol: 29.174 Å2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.478 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.72→40 Å
| ||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||
Xplor file |
|