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- PDB-1tqo: Cryogenic Crystal Structure of Staphylococcal Nuclease Variant tr... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1tqo | ||||||
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Title | Cryogenic Crystal Structure of Staphylococcal Nuclease Variant truncated Delta+PHS I92E | ||||||
![]() | 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 | ![]() ![]() | ||||||
![]() | Nguyen, D.M. / Reynald, R.L. / Gittis, A.G. / Lattman, E.E. | ||||||
![]() | ![]() Title: X-ray and thermodynamic studies of staphylococcal nuclease variants I92E and I92K: insights into polarity of the protein interior Authors: Nguyen, D.M. / Reynald, R.L. / Gittis, A.G. / Lattman, E.E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 40.7 KB | Display | ![]() |
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PDB format | ![]() | 27.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1tr5C ![]() 1tt2C ![]() 1sncS 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: 15700.994 Da / Num. of mol.: 1 / Mutation: G50F, V51N, I92E, P117G, H124L, S128A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49 % |
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Crystal grow![]() | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 6 Details: MPD, potassium phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 27K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 20, 2000 / Details: mirrors |
Radiation | Monochromator: OSMIC MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2→19.3 Å / Num. all: 10439 / Num. obs: 10439 / % possible obs: 99.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6 % / Biso Wilson estimate: 17.7 Å2 / Rmerge(I) obs: 0.051 / Rsym value: 0.051 / Net I/σ(I): 15.81 |
Reflection shell | Resolution: 2→2.13 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.096 / Mean I/σ(I) obs: 4.81 / Num. unique all: 1561 / Rsym value: 0.096 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 1SNC Resolution: 2→19.13 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1039797.01 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 43.7814 Å2 / ksol: 0.368584 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→19.13 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
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Xplor file |
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