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Yorodumi- PDB-4rkb: Crystal structure of Staphylococcal nuclease variant Delta+PHS V6... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4rkb | ||||||
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Title | Crystal structure of Staphylococcal nuclease variant Delta+PHS V66T/V99T at cryogenic temperature | ||||||
Components | Thermonuclease | ||||||
Keywords | HYDROLASE / Staphylococcal nuclease / hyperstable variant / pdtp / cavity / pressure | ||||||
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 / membrane / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.88 Å | ||||||
Authors | Caro, J.A. / Schlessman, J.L. / Garcia-Moreno E., B. | ||||||
Citation | Journal: to be published Title: Cavities in proteins Authors: Caro, J.A. / Schlessman, J.L. / 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 | 4rkb.cif.gz | 44.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4rkb.ent.gz | 28.6 KB | Display | PDB format |
PDBx/mmJSON format | 4rkb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4rkb_validation.pdf.gz | 780.7 KB | Display | wwPDB validaton report |
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Full document | 4rkb_full_validation.pdf.gz | 781.6 KB | Display | |
Data in XML | 4rkb_validation.xml.gz | 8.3 KB | Display | |
Data in CIF | 4rkb_validation.cif.gz | 10.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rk/4rkb ftp://data.pdbj.org/pub/pdb/validation_reports/rk/4rkb | HTTPS FTP |
-Related structure data
Related structure data | 4k5vC 4kjnC 4kjoC 4me5C 4miuC 4n9pC 4n9tC 4nmzC 4r8nC 4rklC 3bdcS S: Starting model for refinement C: citing same article (ref.) |
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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: 16147.408 Da / Num. of mol.: 1 / Fragment: UNP residues 83-232 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: nuc / Plasmid: pET24a+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00644, micrococcal nuclease |
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#2: Chemical | ChemComp-THP / |
#3: Chemical | ChemComp-CA / |
#4: 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: 2.2 Å3/Da / Density % sol: 44.1 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 30% MPD, 25 mM Potassium Phosphate, Calcium Chloride, pdTp , pH 9, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 277 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: APEX II CCD / Detector: CCD / Date: Jan 23, 2014 / Details: Multilayer | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: GE111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.88→60.54 Å / Num. all: 11479 / Num. obs: 11479 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.64 % / Biso Wilson estimate: 32.6 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 26.46 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3BDC Resolution: 1.88→37.89 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.938 / WRfactor Rfree: 0.2154 / WRfactor Rwork: 0.1793 / FOM work R set: 0.8345 / SU B: 3.39 / SU ML: 0.1 / SU R Cruickshank DPI: 0.1512 / SU Rfree: 0.1398 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.151 / ESU R Free: 0.14 / 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: 76.56 Å2 / Biso mean: 27.027 Å2 / Biso min: 12.96 Å2
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Refinement step | Cycle: LAST / Resolution: 1.88→37.89 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.88→1.929 Å / Total num. of bins used: 20
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