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Yorodumi- PDB-2e52: Crystal structural analysis of HindIII restriction endonuclease i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2.0E+52 | ||||||
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Title | Crystal structural analysis of HindIII restriction endonuclease in complex with cognate DNA at 2.0 angstrom resolution | ||||||
Components |
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Keywords | hydrolase/DNA / Type II restriction enzyme HindIII(E.C.3.1.21.4)/DNA / hydrolase-DNA COMPLEX | ||||||
Function / homology | Function and homology information type II site-specific deoxyribonuclease / type II site-specific deoxyribonuclease activity / DNA restriction-modification system Similarity search - Function | ||||||
Biological species | Haemophilus influenzae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å | ||||||
Authors | Watanabe, N. / Sato, C. / Tanaka, I. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2009 Title: Structures of restriction endonuclease HindIII in complex with its cognate DNA and divalent cations Authors: Watanabe, N. / Takasaki, Y. / Sato, C. / Ando, S. / Tanaka, I. | ||||||
History |
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Remark 650 | HELIX Determination method: Author determined |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2e52.cif.gz | 311 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2e52.ent.gz | 247 KB | Display | PDB format |
PDBx/mmJSON format | 2e52.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e5/2e52 ftp://data.pdbj.org/pub/pdb/validation_reports/e5/2e52 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 34998.172 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Haemophilus influenzae (bacteria) / Strain: Rd KW20 / Gene: hindIIIR / Plasmid: pET16b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)plysS References: UniProt: P43870, type II site-specific deoxyribonuclease #2: DNA chain | Mass: 3663.392 Da / Num. of mol.: 6 / Source method: obtained synthetically #3: Chemical | ChemComp-GOL / #4: Chemical | #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: 2.93 Å3/Da / Density % sol: 58.04 % | ||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 18% PEG 3350, 0.08M Ammonium Acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jun 16, 2006 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→39.684 Å / Num. all: 126130 / Num. obs: 126130 / % possible obs: 100 % / Observed criterion σ(F): -1 / Observed criterion σ(I): -1 / Redundancy: 7.7 % / Biso Wilson estimate: 24.2 Å2 / Rmerge(I) obs: 0.055 / Rsym value: 0.055 / Net I/σ(I): 29.2 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.156 / Mean I/σ(I) obs: 11.8 / Num. unique all: 12567 / Rsym value: 0.156 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2→39.684 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.929 / Rfactor Rfree error: 6327 / SU B: 2.872 / SU ML: 0.084 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.148 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.782 Å2
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Refinement step | Cycle: LAST / Resolution: 2→39.684 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.001→2.053 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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