+Open data
-Basic information
Entry | Database: PDB / ID: 2gii | ||||||
---|---|---|---|---|---|---|---|
Title | Q138F HincII bound to cognate DNA GTTAAC | ||||||
Components |
| ||||||
Keywords | HYDROLASE/DNA / protein DNA complex / indirect readout / DNA intercalation / endonuclease / HYDROLASE-DNA COMPLEX | ||||||
Function / homology | Function and homology information type II site-specific deoxyribonuclease / type II site-specific deoxyribonuclease activity / DNA restriction-modification system / DNA binding Similarity search - Function | ||||||
Biological species | Haemophilus influenzae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Horton, N.C. / Joshi, H.K. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2006 Title: Alteration of Sequence Specificity of the Type II Restriction Endonuclease HincII through an Indirect Readout Mechanism. Authors: Joshi, H.K. / Etzkorn, C. / Chatwell, L. / Bitinaite, J. / Horton, N.C. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2gii.cif.gz | 131.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2gii.ent.gz | 99 KB | Display | PDB format |
PDBx/mmJSON format | 2gii.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gi/2gii ftp://data.pdbj.org/pub/pdb/validation_reports/gi/2gii | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Details | The biological assembly is a protein dimer bound to one duplex of DNA. The asymmetric unit contains the biological assembly. |
-Components
#1: DNA chain | Mass: 4281.779 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Protein | Mass: 29839.109 Da / Num. of mol.: 2 / Mutation: Q138F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: hincIIR / Plasmid: pCCR101HincII.R / Production host: Escherichia coli (E. coli) / Strain (production host): ER2393 References: UniProt: P44413, UniProt: P17743*PLUS, type II site-specific deoxyribonuclease #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.72 % | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 25% PEG 4K, 0.15 M NaCl, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K | ||||||||||||||||||||||||||||||||||||
Components of the solutions |
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL1-5 / Wavelength: 0.9 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 17, 2005 |
Radiation | Monochromator: 180 degrees, 1 degree per frame, 30 sec / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.14→50 Å / Num. all: 32583 / Num. obs: 32583 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 1.9 % / Biso Wilson estimate: 36.4 Å2 / Rmerge(I) obs: 0.051 / Rsym value: 0.051 / Net I/σ(I): 24.8 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→50 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|