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- PDB-7lqa: X-ray radiation damage series on Proteinase K at 277K, multi-conf... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7lqa | ||||||
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Title | X-ray radiation damage series on Proteinase K at 277K, multi-conformer model, dataset 2 (merged) | ||||||
![]() | Proteinase K | ||||||
![]() | HYDROLASE / radiation damage / conformational heterogeneity / protease | ||||||
Function / homology | ![]() peptidase K / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yabukarski, F. / Doukov, T. / Herschlag, D. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Evaluating the impact of X-ray damage on conformational heterogeneity in room-temperature (277 K) and cryo-cooled protein crystals. Authors: Yabukarski, F. / Doukov, T. / Mokhtari, D.A. / Du, S. / Herschlag, D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 345.1 KB | Display | ![]() |
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PDB format | ![]() | 243 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7lfgC ![]() 7ljvC ![]() 7ljwC ![]() 7ljzC ![]() 7lk5C ![]() 7lk6C ![]() 7llpC ![]() 7ln7SC ![]() 7ln8C ![]() 7ln9C ![]() 7lnbC ![]() 7lncC ![]() 7lndC ![]() 7loqC ![]() 7lorC ![]() 7lp6C ![]() 7lplC ![]() 7lpmC ![]() 7lptC ![]() 7lpuC ![]() 7lpvC ![]() 7lq8C ![]() 7lq9C ![]() 7lqbC ![]() 7lqcC ![]() 7ltdC ![]() 7ltiC ![]() 7ltvC ![]() 7lu0C ![]() 7lu1C ![]() 7lu2C ![]() 7lu3C 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: 28958.791 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() | ||||||||
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#2: Chemical | #3: Chemical | ChemComp-CA / | #4: Water | ChemComp-HOH / | Has ligand of interest | N | Sequence details | The residue at position 207 was modeled as aspartate instead of serine because the electron density ...The residue at position 207 was modeled as aspartate instead of serine because the electron density unambiguously indicates an aspartate at this position. | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 39.05 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Proteinase K was dissolved in 10 mM Calcium Chloride, 50 mM Tris pH 7.5 at a final concentration of 30 mg/ml. 1-2 microliters of this protein solution was mixed with an equivalent volume of ...Details: Proteinase K was dissolved in 10 mM Calcium Chloride, 50 mM Tris pH 7.5 at a final concentration of 30 mg/ml. 1-2 microliters of this protein solution was mixed with an equivalent volume of precipitant solution (1.0 M Ammonium Sulfate). |
-Data collection
Diffraction | Mean temperature: 277 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 4, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.88557 Å / Relative weight: 1 |
Reflection | Resolution: 1.02→34.89 Å / Num. obs: 120670 / % possible obs: 100 % / Redundancy: 27.2 % / Biso Wilson estimate: 8.93 Å2 / Rmerge(I) obs: 0.133 / Rpim(I) all: 0.025 / Net I/σ(I): 14.4 |
Reflection shell | Resolution: 1.02→1.04 Å / Redundancy: 19 % / Rmerge(I) obs: 3.41 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 5868 / Rpim(I) all: 0.792 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7LN7 Resolution: 1.02→33.89 Å / SU ML: 0.087 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 11.3875 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 8.9 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.02→33.89 Å
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Refine LS restraints |
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LS refinement shell |
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