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Yorodumi- PDB-3h6m: Crystal structure of Staphylococcal nuclease variant Delta+PHS V1... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3h6m | ||||||
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Title | Crystal structure of Staphylococcal nuclease variant Delta+PHS V104E at cryogenic temperature | ||||||
Components | Thermonuclease | ||||||
Keywords | HYDROLASE / Staphylococcal nuclease / hyperstable variant / pdtp / Calcium / Endonuclease / Membrane / Metal-binding / Nuclease | ||||||
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 Similarity search - Function | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.7 Å | ||||||
Authors | Khangulov, V.S. / Schlessman, J.L. / Heroux, A. / Garcia-Moreno, E.B. | ||||||
Citation | Journal: To be Published Title: Crystal structure of Staphylococcal nuclease variant Delta+PHS V104E at cryogenic temperature Authors: Khangulov, V.S. / Schlessman, J.L. / Heroux, 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 | 3h6m.cif.gz | 44.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3h6m.ent.gz | 29.3 KB | Display | PDB format |
PDBx/mmJSON format | 3h6m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3h6m_validation.pdf.gz | 789.1 KB | Display | wwPDB validaton report |
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Full document | 3h6m_full_validation.pdf.gz | 790.2 KB | Display | |
Data in XML | 3h6m_validation.xml.gz | 8.9 KB | Display | |
Data in CIF | 3h6m_validation.cif.gz | 12 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h6/3h6m ftp://data.pdbj.org/pub/pdb/validation_reports/h6/3h6m | HTTPS FTP |
-Related structure data
Related structure data | 3bdcS 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: 16173.447 Da / Num. of mol.: 1 Mutation: 44-49 deletion, G50F, V51N, V104E, P117G, H124L, S128A 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: 2.22 Å3/Da / Density % sol: 44.48 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 30% MPD, 25 mM Potassium Phosphate, Calcium Chloride, pdTp, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9795 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 15, 2009 Details: Meridionally-bent fused silica mirror with palladium and uncoated stripes |
Radiation | Monochromator: Double silicon(111) crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. obs: 15538 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 11.7 % / Biso Wilson estimate: 25.1 Å2 / Rmerge(I) obs: 0.165 / Rsym value: 0.165 / Net I/σ(I): 19.782 |
Reflection shell | Resolution: 1.7→1.73 Å / Redundancy: 11.7 % / Rmerge(I) obs: 0.165 / Mean I/σ(I) obs: 19.789 / Rsym value: 0.165 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Starting model: PDB ENTRY 3BDC Resolution: 1.7→38.205 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.935 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 1.937 / SU ML: 0.066 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.111 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 49.39 Å2 / Biso mean: 18.556 Å2 / Biso min: 6.06 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→38.205 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20
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