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Yorodumi- PDB-1vrr: Crystal structure of the restriction endonuclease BstYI complex w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1vrr | |||||||||
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Title | Crystal structure of the restriction endonuclease BstYI complex with DNA | |||||||||
Components |
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Keywords | hydrolase/DNA / Enzyme-DNA complex / double helix / hydrolase-DNA COMPLEX | |||||||||
Function / homology | Function and homology information type II site-specific deoxyribonuclease activity / DNA restriction-modification system / magnesium ion binding / DNA binding / identical protein binding Similarity search - Function | |||||||||
Biological species | Geobacillus stearothermophilus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å | |||||||||
Authors | Townson, S.A. / Samuelson, J.C. / Xu, S.Y. / Aggarwal, A.K. | |||||||||
Citation | Journal: Structure / Year: 2005 Title: Implications for Switching Restriction Enzyme Specificities from the Structure of BstYI Bound to a BglII DNA Sequence. Authors: Townson, S.A. / Samuelson, J.C. / Xu, S.Y. / Aggarwal, A.K. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1vrr.cif.gz | 108.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1vrr.ent.gz | 81.4 KB | Display | PDB format |
PDBx/mmJSON format | 1vrr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vr/1vrr ftp://data.pdbj.org/pub/pdb/validation_reports/vr/1vrr | HTTPS FTP |
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-Related structure data
Related structure data | |
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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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Details | The biological assembly is composed of the BstYI dimer (chains A and B) and a 14-mer DNA duplex (chains C and D) |
-Components
#1: DNA chain | Mass: 4277.828 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Protein | Mass: 23222.674 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Type II Restriction Endonuclease BstYI Source: (gene. exp.) Geobacillus stearothermophilus (bacteria) Gene: bstYIR / Plasmid: pACYC,pCEF8,pET21at / Production host: Escherichia coli (E. coli) / Strain (production host): ER2744 References: GenBank: 28864483, UniProt: Q84AF2*PLUS, type II site-specific deoxyribonuclease #3: 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: 3.032 Å3/Da / Density % sol: 57.87 % | ||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 1.0 M sodium citrate, 0.1 M sodium cacodylate, 1.5% 1,2,3-heptanetriol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 110 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.979,0.968 | |||||||||
Detector | Type: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: Sep 3, 2003 | |||||||||
Radiation | Monochromator: channel-cut crystal monochromator with toroidal mirrors Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 2.7→50 Å / Num. obs: 35479 / % possible obs: 67.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.2 % | |||||||||
Reflection shell | Highest resolution: 2.7 Å / % possible all: 10 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.7→50 Å / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→50 Å
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