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Yorodumi- PDB-3e43: Q138F HincII bound to GTTAAC and cocrystallized with 2.5 mM MgCl2 -
+Open data
-Basic information
Entry | Database: PDB / ID: 3.0E+43 | ||||||
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Title | Q138F HincII bound to GTTAAC and cocrystallized with 2.5 mM MgCl2 | ||||||
Components |
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Keywords | HYDROLASE/DNA / protein-DNA complex / endonuclease / indirect readout / Hydrolase / Nuclease / Restriction system / 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 / Resolution: 2.73 Å | ||||||
Authors | Horton, N.C. / Babic, A.C. / Little, E.J. / Manohar, V.M. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 Title: DNA distortion and specificity in a sequence-specific endonuclease. Authors: Babic, A.C. / Little, E.J. / Manohar, V.M. / 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 | 3e43.cif.gz | 128 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3e43.ent.gz | 96.2 KB | Display | PDB format |
PDBx/mmJSON format | 3e43.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e4/3e43 ftp://data.pdbj.org/pub/pdb/validation_reports/e4/3e43 | HTTPS FTP |
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-Related structure data
Related structure data | 3e3yC 3e40C 3e41C 3e42C 3e44C 3e45C 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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Unit cell |
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-Components
#1: 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: hindIIR, HI0512 / Production host: Escherichia coli (E. coli) References: UniProt: P44413, UniProt: P17743*PLUS, type II site-specific deoxyribonuclease #2: DNA chain | Mass: 4281.779 Da / Num. of mol.: 2 / Source method: obtained synthetically #3: Chemical | #4: Water | ChemComp-HOH / | Nonpolymer details | UNX IS EITHER WATER MOLECULE OR MG2+ AND IT IS REFERRED TO AS SOL IN THE RELEVANT PUBLICATIO | |
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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: 2.15 Å3/Da / Density % sol: 42.82 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG 4000, 150 mM NaCl, 10 mM HEPES pH 7.5, 2.5 mM MgCl2, 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: SSRL / Beamline: BL9-2 / Wavelength: 0.913321 Å |
Detector | Date: Jul 13, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.913321 Å / Relative weight: 1 |
Reflection | Resolution: 2.73→50 Å / Num. all: 15405 / Num. obs: 14388 / % possible obs: 93.4 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 2.9 % / Biso Wilson estimate: 55.5 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 9.7 |
Reflection shell | Highest resolution: 2.73 Å / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2 / % possible all: 94.7 |
-Processing
Software |
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Refinement | Resolution: 2.73→44.741 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.775 / SU ML: 0.45 / σ(F): 1.36 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 56.226 Å2 / ksol: 0.363 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 99.77 Å2 / Biso mean: 53.567 Å2 / Biso min: 24.04 Å2
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Refinement step | Cycle: LAST / Resolution: 2.73→44.741 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5
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