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- PDB-1dc1: RESTRICTION ENZYME BSOBI/DNA COMPLEX STRUCTURE: ENCIRCLEMENT OF T... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1dc1 | ||||||
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Title | RESTRICTION ENZYME BSOBI/DNA COMPLEX STRUCTURE: ENCIRCLEMENT OF THE DNA AND HISTIDINE-CATALYZED HYDROLYSIS WITHIN A CANONICAL RESTRICTION ENZYME FOLD | ||||||
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![]() | HYDROLASE/DNA / PROTEIN-DNA COMPLEX / RESTRICTION ENDONUCLEASE / THERMOPHILIC ENZYME / DEGENERATE DNA RECOGNITION / HYDROLASE-DNA COMPLEX | ||||||
Function / homology | ![]() type II site-specific deoxyribonuclease / type II site-specific deoxyribonuclease activity / DNA restriction-modification system / DNA binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | van der Woerd, M.J. / Pelletier, J.J. / Xu, S.-Y. / Friedman, A.M. | ||||||
![]() | ![]() Title: Restriction enzyme BsoBI-DNA complex: a tunnel for recognition of degenerate DNA sequences and potential histidine catalysis. Authors: van der Woerd, M.J. / Pelletier, J.J. / Xu, S. / Friedman, A.M. #1: ![]() Title: Cloning and sequence comparison of AvaI and BsoBI restriction modification systems Authors: Ruan, H. / Lunnen, K.D. / Scott, M.E. / Moran, L.S. / Slatko, B.E. / Pelletier, J.J. / Hess, E.J. / Benner II, J. / Wilson, G.G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 161.2 KB | Display | ![]() |
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PDB format | ![]() | 124.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 459.9 KB | Display | ![]() |
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Full document | ![]() | 473.1 KB | Display | |
Data in XML | ![]() | 30.9 KB | Display | |
Data in CIF | ![]() | 45.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: DNA chain | Mass: 3965.609 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: DNA SEQUENCE DESIGNED FOR CRYSTALLIZATION BASED ON THE CENTRAL RECOGNITION SEQUENCE OF BACILLUS STEAROTHERMOPHILUS #2: Protein | Mass: 36742.793 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() References: UniProt: P70985, type II site-specific deoxyribonuclease #3: Chemical | ChemComp-DIO / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.2 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.6 Details: EQUILIBRATION AGAINST RESERVOIR OF 20% (V/V) DIOXANE, 2% (V/V) ETHYLENE GLYCOL AND 5 MM DTT. DROPS WERE FORMED BY MIXING 2.5 UL PROTEIN-DNA COMPLEX (10 MG/ML PROTEIN; 1.1 FOLD MOLAR EXCESS ...Details: EQUILIBRATION AGAINST RESERVOIR OF 20% (V/V) DIOXANE, 2% (V/V) ETHYLENE GLYCOL AND 5 MM DTT. DROPS WERE FORMED BY MIXING 2.5 UL PROTEIN-DNA COMPLEX (10 MG/ML PROTEIN; 1.1 FOLD MOLAR EXCESS DNA) IN BUFFER (20 MM TRIS-HCL PH 7.6, 300 MM NACL, 0.1 MM EDTA, 1 MM DTT, 0.02% NA AZIDE) WITH 2.5 UL DISTILLED WATER, 2.5 UL RESERVOIR SOLUTION AND 1.5 UL 350 MM N-HEPTYL-B-D-GLUCOSIDE, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Sep 1, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→30 Å / Num. all: 77509 / Num. obs: 77509 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 20.9 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 24.5 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.519 / Mean I/σ(I) obs: 2.1 / % possible all: 95.4 |
Reflection | *PLUS |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Stereochemistry target values: ENGH & HUBER AND PARKINSON ET AL.
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Displacement parameters | Biso mean: 23.33 Å2
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Refine analyze | Luzzati coordinate error obs: 0.197 Å / Luzzati d res low obs: 8 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→8 Å
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Refine LS restraints |
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Refine LS restraints NCS | Rms dev position: 0.0991 Å / Weight Biso : 300 / Weight position: 2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.7→1.78 Å / Total num. of bins used: 8
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 8 Å / σ(F): 2 / % reflection Rfree: 5.1 % / Rfactor obs: 0.19 / Rfactor Rwork: 0.19 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_deg / Dev ideal: 1.6 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.45 / % reflection Rfree: 5 % / Rfactor Rwork: 0.402 |