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- PDB-4miu: 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: 4miu | ||||||
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Title | Crystal structure of Staphylococcal nuclease variant Delta+PHS V23T/V99T 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 | ![]() ![]() ![]() | ||||||
![]() | 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 | ![]() | 46.3 KB | Display | ![]() |
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PDB format | ![]() | 30.5 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 ![]() 4me5C ![]() 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: 16147.408 Da / Num. of mol.: 1 / Fragment: Nuclease A (UNP residues 83-231) / Mutation: V23T, G50F,V51N,V99T,P117G,H124L,S128A,del(44-49) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-THP / ![]() |
#3: Chemical | ChemComp-CA / |
#4: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.88 % |
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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, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 110 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![]() |
Reflection | Resolution: 1.67→50 Å / Num. all: 16555 / Num. obs: 16555 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.7 % / Biso Wilson estimate: 29.9 Å2 / Rmerge(I) obs: 0.015 / Net I/σ(I): 46.5 |
Reflection shell | Resolution: 1.67→1.77 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.184 / Mean I/σ(I) obs: 5.1 / Num. unique all: 2612 / % 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: 1.67→38.14 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.947 / WRfactor Rfree: 0.2093 / WRfactor Rwork: 0.1646 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.818 / SU B: 2.379 / SU ML: 0.079 / SU R Cruickshank DPI: 0.1065 / SU Rfree: 0.1123 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.107 / ESU R Free: 0.112 / 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: 64.96 Å2 / Biso mean: 24.0906 Å2 / Biso min: 11.46 Å2
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Refinement step | Cycle: LAST / Resolution: 1.67→38.14 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.67→1.713 Å / Total num. of bins used: 20
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