+Open data
-Basic information
Entry | Database: PDB / ID: 4pxg | ||||||
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Title | Crystal Structure of TypeII restriction Enzyme Sau3AI | ||||||
Components | Type-2 restriction enzyme Sau3AI | ||||||
Keywords | HYDROLASE / Type II restriction enzyme | ||||||
Function / homology | Function and homology information type II site-specific deoxyribonuclease / type II site-specific deoxyribonuclease activity / DNA restriction-modification system / DNA binding Similarity search - Function | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.45 Å | ||||||
Authors | Xu, C.Y. / Yu, F. / Hu, X.J. / He, J.H. | ||||||
Citation | Journal: To be Published Title: The 2.45 A Crystal Structure of the Restriction Endonuclease Sau3AI Suggests a Self-Inhibition Mechanism Authors: Xu, C.Y. / Yu, F. / Hu, X.J. / He, J.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4pxg.cif.gz | 195.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4pxg.ent.gz | 163.5 KB | Display | PDB format |
PDBx/mmJSON format | 4pxg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/px/4pxg ftp://data.pdbj.org/pub/pdb/validation_reports/px/4pxg | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
#1: Protein | Mass: 59089.082 Da / Num. of mol.: 2 / Mutation: E64A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: 3A / Gene: sau3AIR / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): B834 References: UniProt: P16667, type II site-specific deoxyribonuclease #2: Chemical | ChemComp-CA / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.89 Å3/Da / Density % sol: 57.47 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 16% polyethylene glycol 8000, 1M sodium acetate, 0.2M calcium chloride, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 2.45→54.14 Å / Num. all: 47905 / Num. obs: 47905 / % possible obs: 8.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 11.6 % / Rmerge(I) obs: 0.062 / Rsym value: 0.062 | |||||||||||||||||||||
Reflection shell | Diffraction-ID: 1,2
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-Processing
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Refinement | Method to determine structure: SAD / Resolution: 2.45→50 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.914 / SU B: 11.307 / SU ML: 0.245 / Cross valid method: THROUGHOUT / ESU R: 0.432 / ESU R Free: 0.28 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 71.955 Å2
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Refinement step | Cycle: LAST / Resolution: 2.45→50 Å
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Refine LS restraints |
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