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- PDB-3v1z: Crystal structure of Type IIF restriction endonuclease Bse634I wi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3v1z | ||||||
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Title | Crystal structure of Type IIF restriction endonuclease Bse634I with cognate DNA | ||||||
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![]() | Hydrolase/DNA / RESTRICTION ENDONUCLEASE / protein-DNA complex / HYDROLASE / Hydrolase-DNA complex | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Manakova, E.N. / Grazulis, S. / Golovenko, D. / Tamulaitiene, G. | ||||||
![]() | ![]() Title: Structural mechanisms of the degenerate sequence recognition by Bse634I restriction endonuclease. Authors: Manakova, E. / Grazulis, S. / Zaremba, M. / Tamulaitiene, G. / Golovenko, D. / Siksnys, V. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 275.7 KB | Display | ![]() |
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PDB format | ![]() | 221.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 443 KB | Display | ![]() |
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Full document | ![]() | 445.4 KB | Display | |
Data in XML | ![]() | 24.3 KB | Display | |
Data in CIF | ![]() | 34.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3v20C ![]() 3v21C ![]() 1knvS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 33762.758 Da / Num. of mol.: 2 / Mutation: R226A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: 1422 / Gene: bse634IR / Plasmid: pUC18 / Production host: ![]() ![]() References: UniProt: Q8RT53, type II site-specific deoxyribonuclease #2: DNA chain | Mass: 3969.561 Da / Num. of mol.: 2 / Source method: obtained synthetically #3: Water | ChemComp-HOH / | Sequence details | AUTHORS STATE THAT THE RESIDUES AT POSITION 110, 111, AND 130 ARE CORRECTLY IDENTIFIED AND THE ...AUTHORS STATE THAT THE RESIDUES AT POSITION 110, 111, AND 130 ARE CORRECTLY IDENTIFIED | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 49.2 % |
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Crystal grow | Temperature: 293 K / pH: 5.5 Details: 100mM Na-acetate pH 4.25-5.5, 10mM CaCl2 or CaAc2, 4-8% (w/v) of PEG8000, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 7, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→69.14 Å / Num. obs: 33372 / % possible obs: 99.1 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 39.35 Å2 / Rmerge(I) obs: 0.067 / Rsym value: 0.067 / Net I/σ(I): 16.7 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.307 / Mean I/σ(I) obs: 2.5 / Rsym value: 0.307 / % possible all: 95.2 |
-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Starting model: PDB ENTRY 1KNV Resolution: 2.2→62.14 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.888 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 17.142 / SU ML: 0.198 / SU R Cruickshank DPI: 0.366 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.366 / ESU R Free: 0.266 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
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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: 42.3 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→62.14 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.26 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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