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- PDB-5j1z: Crystal structure of Staphylococcal nuclease variant Delta+PHS A9... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5j1z | ||||||
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Title | Crystal structure of Staphylococcal nuclease variant Delta+PHS A90D at cryogenic temperature | ||||||
![]() | Thermonuclease![]() | ||||||
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Function / homology | ![]() endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 3'-phosphomonoesters / ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Skerritt, L.A. / Schlessman, J.L. / Garcia-Moreno E., B. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structure of Staphylococcal nuclease variant Delta+PHS A90D at cryogenic temperature Authors: Skerritt, L.A. / Schlessman, J.L. / Garcia-Moreno E., B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 72.9 KB | Display | ![]() |
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PDB format | ![]() | 51.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3bdcS 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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Unit cell |
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Components
#1: Protein | ![]() Mass: 16187.475 Da / Num. of mol.: 1 / Fragment: UNP residues 83-231 / Mutation: G50F/V51N/A90D/P117G/H124L/S128A/Del44-49 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-CA / |
#3: Chemical | ChemComp-THP / ![]() |
#4: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.82 % |
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Crystal grow![]() | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 20% MPD, 25 mM potassium phosphate, calcium chloride, pdTp |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SEALED TUBE / Type: OTHER / Wavelength: 1.5418 Å |
Detector | Type: AGILENT ATLAS CCD / Detector: CCD / Date: Mar 1, 2016 |
Radiation | Monochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.73→50 Å / Num. obs: 14951 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.2 % / Biso Wilson estimate: 24.55 Å2 / Rmerge(I) obs: 0.019 / Net I/σ(I): 49.13 |
Reflection shell | Resolution: 1.73→1.79 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.117 / Mean I/σ(I) obs: 6.89 / % possible all: 100 |
-Phasing
Phasing![]() | Method: ![]() | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB entry 3BDC Resolution: 1.73→38.35 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.943 / SU B: 4.228 / SU ML: 0.077 / SU R Cruickshank DPI: 0.1075 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.107 / ESU R Free: 0.108 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 52.08 Å2 / Biso mean: 19.249 Å2 / Biso min: 8.88 Å2
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Refinement step | Cycle: final / Resolution: 1.73→38.35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.73→1.775 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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