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- PDB-4kd3: Crystal structure of Staphylococcal nuclease variant Delta+PHS L2... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4kd3 | ||||||
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Title | Crystal structure of Staphylococcal nuclease variant Delta+PHS L25A/V66A/I92A 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 Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Caro, J.A. / Schlessman, J.L. / Heroux, A. / Garcia-Moreno E., B. | ||||||
![]() | ![]() Title: Pressure effects 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 | ![]() | 46.4 KB | Display | ![]() |
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PDB format | ![]() | 30.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 803.6 KB | Display | ![]() |
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Full document | ![]() | 804.9 KB | Display | |
Data in XML | ![]() | 8.8 KB | Display | |
Data in CIF | ![]() | 11.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3v2tC ![]() 4df7C ![]() 4dfaC ![]() 4dgzC ![]() 4du9C ![]() 4f7xC ![]() 4f8mC ![]() 4k5wC ![]() 4kd4C ![]() 4nklC ![]() 4np5C ![]() 4odgC ![]() 4qf4C ![]() 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: 16031.248 Da / Num. of mol.: 1 / Fragment: Nuclease A (UNP residues 83-231) Mutation: L25A,G50F,V51N,V66A,I92A,P117G,H124L,S128A,del(44-49) 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: 44.87 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 20% MPD, 25 mM potassium phosphate, calcium chloride, pdTp, pH 6.0, vapor diffusion, hanging drop, temperature 277K, VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 25, 2011 Details: Meridionally-bent fused silica mirror with palladium and uncoated stripes verti cally-focusing at 6.6:1 demagnification | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double crystal Si(111) with cryogenically-cooled first crystal and sagittally-bent second crystal horizontally-focusing at 3.3:1 demagnification Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.75→50 Å / Num. all: 14281 / Num. obs: 14281 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Biso Wilson estimate: 34.3 Å2 / Rmerge(I) obs: 0.043 / Χ2: 1.542 / Net I/σ(I): 21 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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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 3BDC Resolution: 1.75→38.34 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.95 / WRfactor Rfree: 0.2482 / WRfactor Rwork: 0.2034 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8355 / SU B: 2.538 / SU ML: 0.083 / SU R Cruickshank DPI: 0.1201 / SU Rfree: 0.1167 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.12 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
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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: 90.09 Å2 / Biso mean: 28.9653 Å2 / Biso min: 15.3 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→38.34 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.792 Å / Total num. of bins used: 20
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