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Yorodumi- PDB-7ltv: X-ray radiation damage series on Proteinase K at 100K, crystal st... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ltv | ||||||
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Title | X-ray radiation damage series on Proteinase K at 100K, crystal structure, dataset 3 | ||||||
Components | Proteinase K | ||||||
Keywords | HYDROLASE / radiation damage / conformational heterogeneity / protease | ||||||
Function / homology | Function and homology information peptidase K / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding Similarity search - Function | ||||||
Biological species | Parengyodontium album (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.95 Å | ||||||
Authors | Yabukarski, F. / Doukov, T. / Herschlag, D. | ||||||
Funding support | United States, 1items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2022 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ltv.cif.gz | 237.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ltv.ent.gz | 161.4 KB | Display | PDB format |
PDBx/mmJSON format | 7ltv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ltv_validation.pdf.gz | 432.8 KB | Display | wwPDB validaton report |
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Full document | 7ltv_full_validation.pdf.gz | 433.4 KB | Display | |
Data in XML | 7ltv_validation.xml.gz | 17.1 KB | Display | |
Data in CIF | 7ltv_validation.cif.gz | 28.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lt/7ltv ftp://data.pdbj.org/pub/pdb/validation_reports/lt/7ltv | HTTPS FTP |
-Related structure data
Related structure data | 7lfgC 7ljvC 7ljwC 7ljzC 7lk5C 7lk6C 7llpC 7ln7C 7ln8C 7ln9C 7lnbC 7lncC 7lndC 7loqC 7lorC 7lp6C 7lplC 7lpmC 7lptC 7lpuC 7lpvC 7lq8C 7lq9C 7lqaC 7lqbC 7lqcC 7ltdSC 7ltiC 7lu0C 7lu1C 7lu2C 7lu3C C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 28958.791 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Parengyodontium album (fungus) / References: UniProt: P06873, peptidase K | ||||||||
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#2: Chemical | ChemComp-CA / | ||||||||
#3: Chemical | ChemComp-NO3 / #4: Water | ChemComp-HOH / | Has ligand of interest | N | Has protein modification | Y | 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. This is consistent with other high-resolution crystal structures with aspartate at this position | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.86 % |
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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 (0.5 M Sodium Nitrate). |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.88557 Å |
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: 0.95→34.84 Å / Num. obs: 148367 / % possible obs: 99.9 % / Redundancy: 7.5 % / Biso Wilson estimate: 8.88 Å2 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.027 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 0.95→0.97 Å / Redundancy: 4.4 % / Rmerge(I) obs: 2.014 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 7155 / Rpim(I) all: 1.055 / % possible all: 98.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7LTD Resolution: 0.95→33.87 Å / SU ML: 0.1036 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.8294 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: 13.53 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.95→33.87 Å
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Refine LS restraints |
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LS refinement shell |
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