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Yorodumi- PDB-1qri: X-RAY STRUCTURE OF THE DNA-ECO RI ENDONUCLEASE COMPLEXES WITH AN ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1qri | ||||||
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Title | X-RAY STRUCTURE OF THE DNA-ECO RI ENDONUCLEASE COMPLEXES WITH AN E144D MUTATION AT 2.7 A | ||||||
Components |
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Keywords | HYDROLASE/DNA / RESTRICTION ENDONUCLEASE / DNA-PROTEIN COMPLEX / SITE-DIRECTED MUTATION / SEQUENCE-SPECIFIC / PROTEIN STRUCTURE / HYDROLASE-DNA COMPLEX | ||||||
Function / homology | Function and homology information type II site-specific deoxyribonuclease / type II site-specific deoxyribonuclease activity / DNA restriction-modification system / magnesium ion binding / DNA binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.6 Å | ||||||
Authors | Choi, J. / Kim, Y. / Greene, P. / Hager, P. / Rosenberg, J.M. | ||||||
Citation | Journal: To be Published Title: X-Ray Structure of the DNA-Eco RI Endonuclease Complexes with the ED144 and RK145 Mutations Authors: Choi, J. / Kim, Y. / Greene, P. / Hager, P. / Rosenberg, J.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qri.cif.gz | 84.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qri.ent.gz | 61.2 KB | Display | PDB format |
PDBx/mmJSON format | 1qri.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qr/1qri ftp://data.pdbj.org/pub/pdb/validation_reports/qr/1qri | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 3967.585 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: Protein | Mass: 29158.143 Da / Num. of mol.: 1 / Fragment: RESIDUES 17-277 / Mutation: GLU144ASP / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P00642 |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.02 Å3/Da / Density % sol: 59.28 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8 Details: PRECIPITANT: 40% PEG 400; 40 MM BTP; PH 8.0; RESERVOIR: 16% PEG 400; 40 MM BTP; PH 6.5; DROP: 5 UL PROTEIN, 2 UL DNA, 1 UL PPT, VAPOR DIFFUSION, SITTING DROP, temperature 277K | ||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: SIEMENS-NICOLET X100 / Detector: AREA DETECTOR |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.62→47.6 Å / Num. all: 12291 / Num. obs: 7508 / % possible obs: 61 % / Observed criterion σ(I): 2 / Redundancy: 7 % / Biso Wilson estimate: 17.04 Å2 / Rmerge(I) obs: 0.072 |
Reflection shell | Resolution: 2.62→2.78 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.133 / % possible all: 10 |
-Processing
Software |
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Refinement | Resolution: 2.6→8 Å / σ(F): 3 / Stereochemistry target values: ENGH & HUBER / Details: 52 WATER MOLECULES FIT INTO DIFFERENCE MAPS /
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Refinement step | Cycle: LAST / Resolution: 2.6→8 Å
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Refine LS restraints |
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