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Yorodumi- PDB-2pyk: Crystal structure of Staphylococcal nuclease variant V66Q/P117G/H... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2pyk | ||||||
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Title | Crystal structure of Staphylococcal nuclease variant V66Q/P117G/H124L/S128A at room temperature | ||||||
Components | Thermonuclease | ||||||
Keywords | HYDROLASE / Staphylococcal nuclease / nuclease / hyperstable variant / internal waters | ||||||
Function / homology | Function and homology information endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 3'-phosphomonoesters / micrococcal nuclease / nucleic acid binding / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Schlessman, J.L. / Abe, C. / Garcia-Moreno, E.B. | ||||||
Citation | Journal: Biophys.J. / Year: 2008 Title: Crystallographic study of hydration of an internal cavity in engineered proteins with buried polar or ionizable groups. Authors: Schlessman, J.L. / Abe, C. / Gittis, A. / Karp, D.A. / Dolan, M.A. / Garcia-Moreno, E.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2pyk.cif.gz | 38.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2pyk.ent.gz | 26.4 KB | Display | PDB format |
PDBx/mmJSON format | 2pyk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2pyk_validation.pdf.gz | 427.7 KB | Display | wwPDB validaton report |
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Full document | 2pyk_full_validation.pdf.gz | 428.6 KB | Display | |
Data in XML | 2pyk_validation.xml.gz | 7.4 KB | Display | |
Data in CIF | 2pyk_validation.cif.gz | 9.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/py/2pyk ftp://data.pdbj.org/pub/pdb/validation_reports/py/2pyk | HTTPS FTP |
-Related structure data
Related structure data | 2pw5C 2pw7C 2pztC 2pzuC 2pzwC 100kS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 16791.275 Da / Num. of mol.: 1 / Mutation: V66Q, P117G, H124L, S128A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: nuc / Plasmid: lambda / Production host: Escherichia coli (E. coli) / Strain (production host): AR120 References: UniProt: Q8NXI6, UniProt: A5A513*PLUS, micrococcal nuclease |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 45.96 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.8 Details: 37% MPD, 0.025 M potassium phosphate, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: SEALED TUBE / Type: OTHER / Wavelength: 1.5418 |
Detector | Type: APEX II CCD / Detector: CCD / Date: Mar 15, 2006 |
Radiation | Monochromator: GE111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. all: 8881 / Num. obs: 8861 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.2 % / Rmerge(I) obs: 0.0229 / Net I/σ(I): 32.85 |
Reflection shell | Resolution: 2.1→2.2 Å / Redundancy: 4.89 % / Rmerge(I) obs: 0.1344 / Mean I/σ(I) obs: 7.09 / Num. unique all: 1141 / % possible all: 100 |
-Phasing
Phasing MR | Cor.coef. Fo:Fc: 0.716 / Packing: 0.52
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Staphyloccocal nuclease V66E/P117G/H124L/S128A variant (at 100K), with b-factors set to 20.0 A^2 and residue 66 truncated to Ala, waters excluded Resolution: 2.1→50 Å / FOM work R set: 0.844 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 64.307 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.354 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→50 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18
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Xplor file |
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