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- PDB-4evo: Crystal structure of Staphylococcal nuclease variant NVIAGA/E122G... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4evo | ||||||
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Title | Crystal structure of Staphylococcal nuclease variant NVIAGA/E122G 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 | ![]() ![]() ![]() ![]() | ||||||
![]() | Doctrow, B.M. / Schlessman, J.L. / Garcia-Moreno E., B. / Heroux, A. | ||||||
![]() | ![]() Title: Local flexibility as a determinant of pKa values of surface ionizable groups in proteins Authors: Doctrow, B.M. / Schlessman, J.L. / Garcia-Moreno E., B. / Baran, K.L. / Chimenti, M.S. / Herbst, K.J. / Fitch, C.A. / Majumdar, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 66.7 KB | Display | ![]() |
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PDB format | ![]() | 48.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3u9oC ![]() 4e6iC ![]() 2rdfS 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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Unit cell |
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Components
#1: Protein | ![]() Mass: 16708.301 Da / Num. of mol.: 1 / Fragment: Nuclease A (UNP residues 83-231) / Mutation: D21N/T33V/T41I/S59A/P117G/E122G/S128A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-PO4 / ![]() |
#3: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.28 % |
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Crystal grow![]() | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 44% MPD, 25 mM potassium phosphate, calcium chloride, pdTp, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 18, 2010 Details: Meridionally-bent fused silica mirror with palladium and uncoated stripes vertically-focusing at 6.6:1 demagnification | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.95→50 Å / Num. all: 10871 / Num. obs: 10871 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.6 % / Biso Wilson estimate: 40.1 Å2 / Rmerge(I) obs: 0.055 / Χ2: 1.83 / Net I/σ(I): 17.9 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-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 2RDF Resolution: 1.95→26.52 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.939 / WRfactor Rfree: 0.2468 / WRfactor Rwork: 0.1997 / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.8353 / SU B: 7.308 / SU ML: 0.105 / SU R Cruickshank DPI: 0.1641 / SU Rfree: 0.152 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.164 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : WITH TLS ADDED
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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: 109.85 Å2 / Biso mean: 42.4968 Å2 / Biso min: 21.32 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→26.52 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 0.191 Å / Origin y: 19.559 Å / Origin z: -0.551 Å
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