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Open data
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Basic information
Entry | Database: PDB / ID: 3wvg | ||||||
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Title | Time-Resolved Crystal Structure of HindIII with 0sec soaking | ||||||
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![]() | HYDROLASE/DNA / FREEZE-TRAP / time-resolved / type IIP restriction endonuclease / restriction endonuclease / hydrolase / nuclease / HYDROLASE-DNA complex | ||||||
Function / homology | ![]() type II site-specific deoxyribonuclease / type II site-specific deoxyribonuclease activity / DNA restriction-modification system Similarity search - Function | ||||||
Biological species | ![]() synthetic (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kawamura, T. / Kobayashi, T. / Watanabe, N. | ||||||
![]() | ![]() Title: Analysis of the HindIII-catalyzed reaction by time-resolved crystallography Authors: Kawamura, T. / Kobayashi, T. / Watanabe, N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 311.2 KB | Display | ![]() |
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PDB format | ![]() | 247.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3wvhC ![]() 3wviC ![]() 3wvkC ![]() 3wvpC ![]() 3a4kS 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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4 | ![]()
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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.) ![]() ![]() ![]() References: UniProt: P43870, type II site-specific deoxyribonuclease #2: DNA chain | Mass: 3663.392 Da / Num. of mol.: 8 / Source method: obtained synthetically Details: This DNA sequence synthesized chemically contains cognate HindIIIR recognition sequence and elongated scaffolds on both side Source: (synth.) synthetic (others) #3: Chemical | ChemComp-NA / #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.99 Å3/Da / Density % sol: 58.83 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 10-15% PEG 3350, 300mM NaSCN, 10% Glycerol, 100mM Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 19, 2013 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→50 Å / Num. obs: 93316 / % possible obs: 99.65 % / Redundancy: 3.7 % / Biso Wilson estimate: 31.4 Å2 / Rmerge(I) obs: 0.128 / Net I/σ(I): 16.5 |
Reflection shell | Resolution: 2.25→2.29 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.892 / Mean I/σ(I) obs: 2.2 / % possible all: 97.74 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 3A4K Resolution: 2.25→39.7 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.931 / SU B: 6.02 / SU ML: 0.144 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.225 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 122.43 Å2 / Biso mean: 38.386 Å2 / Biso min: 12.31 Å2
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Refinement step | Cycle: LAST / Resolution: 2.25→39.7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.254→2.312 Å / Total num. of bins used: 20
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