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- PDB-4me5: Crystal structure of Staphylococcal nuclease variant Delta+PHS V2... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4me5 | ||||||
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Title | Crystal structure of Staphylococcal nuclease variant Delta+PHS V23S/V66A at cryogenic temperature | ||||||
![]() | Thermonuclease | ||||||
![]() | HYDROLASE / Staphylococcal nuclease / hyperstable variant / pdtp / cavity / pressure | ||||||
Function / homology | ![]() endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 3'-phosphomonoesters / micrococcal nuclease / nucleic acid binding / extracellular region / membrane / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Caro, J.A. / Schlessman, J.L. / Garcia-Moreno E., B. | ||||||
![]() | ![]() Title: Cavities in proteins Authors: Caro, J.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 | ![]() | 71.5 KB | Display | ![]() |
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PDB format | ![]() | 51.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4k5vC ![]() 4kjnC ![]() 4kjoC ![]() 4miuC ![]() 4n9pC ![]() 4n9tC ![]() 4nmzC ![]() 4r8nC ![]() 4rkbC ![]() 4rklC ![]() 3bdcS S: Starting model for refinement C: citing same article ( |
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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: 16103.357 Da / Num. of mol.: 1 / Fragment: Nuclease A (UNP residues 83-231) / Mutation: V23S, G50F,V51N,V66A,P117G,H124L,S128A 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: 2.22 Å3/Da / Density % sol: 44.62 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 25% 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: SEALED TUBE / Type: BRUKER / Wavelength: 1.54 Å |
Detector | Type: APEX II CCD / Detector: CCD / Date: Jan 25, 2013 / Details: Multilayer |
Radiation | Monochromator: Ge(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. all: 13154 / Num. obs: 13154 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.7 % / Biso Wilson estimate: 26.7 Å2 / Rmerge(I) obs: 0.033 / Net I/σ(I): 23.8 |
Reflection shell | Resolution: 1.8→1.89 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.261 / Mean I/σ(I) obs: 3.7 / Num. unique all: 1789 / % 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: 1.8→38.05 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.931 / WRfactor Rfree: 0.2044 / WRfactor Rwork: 0.1569 / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.8522 / SU B: 4.486 / SU ML: 0.081 / SU R Cruickshank DPI: 0.1262 / SU Rfree: 0.132 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.126 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 59.99 Å2 / Biso mean: 20.7591 Å2 / Biso min: 10.13 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→38.05 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 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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