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- PDB-3e5s: Crystal structure of Staphylococcal nuclease variant Delta+PHS L1... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3e5s | ||||||
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Title | Crystal structure of Staphylococcal nuclease variant Delta+PHS L103K 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 | ![]() ![]() ![]() | ||||||
![]() | Khangulov, V.S. / Schlessman, J.L. / Garcia-Moreno, E.B. | ||||||
![]() | ![]() Title: Crystal structure of Staphylococcal nuclease variant Delta+PHS L103K at cryogenic temperature Authors: Khangulov, V.S. / 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 | ![]() | 71.5 KB | Display | ![]() |
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PDB format | ![]() | 51.6 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | ![]() Mass: 16159.486 Da / Num. of mol.: 2 / Mutation: G50F/V51N/L103K/P117G/H124L/S128A/Del44-49 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() ![]() #2: Chemical | ![]() #3: Chemical | #4: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.7 % |
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Crystal grow![]() | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 35% MPD, 25 mM Potassium Phosphate, Calcium Chloride, pdTp, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SEALED TUBE / Type: OTHER / Wavelength: 1.5418 Å | ||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: APEX II CCD / Detector: CCD / Date: Jul 31, 2007 / Details: multi-layer optics | ||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: GE111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength![]() | ||||||||||||||||||||||||||||||||||||||||||||
Reflection | Redundancy: 5.05 % / Av σ(I) over netI: 19.83 / Number: 121434 / Rsym value: 0.103 / D res high: 1.859 Å / Num. obs: 24053 / % possible obs: 97.65 | ||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 1.859→60.95 Å / Num. all: 24646 / Num. obs: 24052 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.92 % / Biso Wilson estimate: 21.1 Å2 / Rmerge(I) obs: 0.0658 / Rsym value: 0.0739 / Net I/σ(I): 15.7 | ||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Resolution: 1.859→1.96 Å / Redundancy: 2.19 % / Rmerge(I) obs: 0.3219 / Mean I/σ(I) obs: 2.48 / Num. unique all: 3521 / Rsym value: 0.4179 / % possible all: 91.1 |
-Phasing
Phasing![]() | Method: ![]() | |||||||||
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Phasing MR | Rfactor: 47.72 / Model details: Phaser MODE: MR_AUTO
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 3BDC.PDB Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.882 / Highest resolution: 2 Å / WRfactor Rfree: 0.205 / WRfactor Rwork: 0.159 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.905 / SU B: 2.575 / SU ML: 0.073 / SU R Cruickshank DPI: 0.035 / SU Rfree: 0.034 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.035 / ESU R Free: 0.034 / Stereochemistry target values: Engh & Huber / 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 / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 49.01 Å2 / Biso mean: 14.49 Å2 / Biso min: 0 Å2
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Refine analyze | Luzzati coordinate error obs: 0.1875 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 2 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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