+Open data
-Basic information
Entry | Database: PDB / ID: 1xhv | ||||||
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Title | HincII bound to cleaved cognate DNA GTCGAC and Mn2+ | ||||||
Components |
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Keywords | hydrolase/DNA / restriction endonuclease / phosphoryl transfer / 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: 2.5 Å | ||||||
Authors | Etzkorn, C. / Horton, N.C. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2004 Title: Mechanistic Insights from the Structures of HincII Bound to Cognate DNA Cleaved from Addition of Mg(2+) and Mn(2+) Authors: Etzkorn, C. / Horton, N.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1xhv.cif.gz | 273.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1xhv.ent.gz | 213.8 KB | Display | PDB format |
PDBx/mmJSON format | 1xhv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xh/1xhv ftp://data.pdbj.org/pub/pdb/validation_reports/xh/1xhv | HTTPS FTP |
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-Related structure data
Related structure data | 1xhuC 1kc6S 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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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: DNA chain | Mass: 2114.398 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: phosphoramidite synthetic chemistry #2: DNA chain | Mass: 1834.230 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: phosphoramidite synthetic chemistry #3: Protein | Mass: 29820.066 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: hincIIR / Production host: Escherichia coli (E. coli) References: UniProt: P17743, type II site-specific deoxyribonuclease #4: Chemical | ChemComp-MN / #5: 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: 2.83 Å3/Da / Density % sol: 56.6 % | ||||||||||||||||
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: PEG 4000, NaCl, citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K | ||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-BM / Wavelength: 0.9 Å |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 53281 / % possible obs: 89.3 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Biso Wilson estimate: 58.3 Å2 / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / Net I/σ(I): 16.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1KC6 without solvent Resolution: 2.5→50 Å / Cross valid method: R free / σ(F): 2 / Stereochemistry target values: as in CNS
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Refinement step | Cycle: LAST / Resolution: 2.5→50 Å
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Refine LS restraints |
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