+Open data
-Basic information
Entry | Database: PDB / ID: 2gie | ||||||
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Title | HincII bound to cognate DNA GTTAAC | ||||||
Components |
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Keywords | HYDROLASE/DNA / protein DNA complex / indirect readout / DNA intercalation / 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: 2.6 Å | ||||||
Authors | Horton, N.C. / Joshi, H.K. / Etzkorn, C. / Chatwell, L. / Bitinaite, J. | ||||||
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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2gie.cif.gz | 255.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2gie.ent.gz | 201.7 KB | Display | PDB format |
PDBx/mmJSON format | 2gie.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2gie_validation.pdf.gz | 489.9 KB | Display | wwPDB validaton report |
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Full document | 2gie_full_validation.pdf.gz | 534.1 KB | Display | |
Data in XML | 2gie_validation.xml.gz | 49.3 KB | Display | |
Data in CIF | 2gie_validation.cif.gz | 69.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gi/2gie ftp://data.pdbj.org/pub/pdb/validation_reports/gi/2gie | HTTPS FTP |
-Related structure data
Related structure data | 2gigC 2gihC 2giiC 2gijC 1tx3S 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
#1: DNA chain | Mass: 3992.598 Da / Num. of mol.: 4 / Source method: obtained synthetically #2: 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 / 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: Chemical | ChemComp-NA / | #4: 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: 2.75 Å3/Da / Density % sol: 55.33 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 25% PEG 4K, 0.15 M NaCl, 0.1 M 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: 14-BM-C / Wavelength: 0.9 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 3, 2003 |
Radiation | Monochromator: 180 frames, 1 degree oscillation each, 100 sec Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. obs: 46277 / % possible obs: 97.4 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 62.5 Å2 / Rmerge(I) obs: 0.095 / Rsym value: 0.095 / Net I/σ(I): 11 |
Reflection shell | Resolution: 2.6→2.69 Å / Rmerge(I) obs: 0.952 / Mean I/σ(I) obs: 2 / % possible all: 95.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1TX3 Resolution: 2.6→50 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.6→50 Å
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Refine LS restraints |
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