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Open data
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Basic information
Entry | Database: PDB / ID: 1xhu | ||||||
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Title | HincII bound to cleaved, cognate DNA containing GTCGAC | ||||||
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![]() | hydrolase/DNA / restriction endonuclease / phosphoryl transfer / hydrolase-DNA COMPLEX | ||||||
Function / homology | ![]() type II site-specific deoxyribonuclease / type II site-specific deoxyribonuclease activity / DNA restriction-modification system / DNA binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Etzkorn, C. / Horton, N.C. | ||||||
![]() | ![]() 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. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 257 KB | Display | ![]() |
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PDB format | ![]() | 202.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 427 KB | Display | ![]() |
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Full document | ![]() | 485.8 KB | Display | |
Data in XML | ![]() | 29.3 KB | Display | |
Data in CIF | ![]() | 47.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1xhvC ![]() 1kc6S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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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.) ![]() ![]() ![]() References: UniProt: P17743, type II site-specific deoxyribonuclease #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.82 Å3/Da / Density % sol: 56.4 % | ||||||||||||||||
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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: ![]() ![]() ![]() |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.95→50 Å / Num. obs: 27364 / % possible obs: 85.4 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 2.3 % / Biso Wilson estimate: 46.2 Å2 / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Net I/σ(I): 6.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1KC6 with water removed Resolution: 2.95→50 Å / Cross valid method: R free / σ(F): 3 / Stereochemistry target values: as in CNS
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Refinement step | Cycle: LAST / Resolution: 2.95→50 Å
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Refine LS restraints |
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