+Open data
-Basic information
Entry | Database: PDB / ID: 4da2 | ||||||
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Title | The structure of Pyrococcus Furiosus SfsA in complex with Ca2+ | ||||||
Components | Sugar fermentation stimulation protein homolog | ||||||
Keywords | DNA BINDING PROTEIN / OB fold / PD-(D/E)xK domain / nuclease | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Pyrococcus furiosus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å | ||||||
Authors | Baker, P.J. / Allen, F.L. | ||||||
Citation | Journal: To be Published Title: The structure of SfsA and its DNA complex; A DNA/RNA nuclease with a novel domain combination Authors: Allen, F.L. / Akerboom, J. / Bliss, S.J. / Blombach, F. / Sedelnikova, S.E. / van der Oost, J. / Baker, P.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4da2.cif.gz | 103.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4da2.ent.gz | 83.6 KB | Display | PDB format |
PDBx/mmJSON format | 4da2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4da2_validation.pdf.gz | 419.1 KB | Display | wwPDB validaton report |
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Full document | 4da2_full_validation.pdf.gz | 419.5 KB | Display | |
Data in XML | 4da2_validation.xml.gz | 18.8 KB | Display | |
Data in CIF | 4da2_validation.cif.gz | 26.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/da/4da2 ftp://data.pdbj.org/pub/pdb/validation_reports/da/4da2 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 26229.098 Da / Num. of mol.: 2 / Mutation: L120I Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / Gene: PF1198, sfsA / Plasmid: pET24d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8U1K8 #2: Chemical | ChemComp-CA / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.75 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion / pH: 4.6 Details: 30% (w/v) PEG 3350, 0.2 M calcium acetate, 0.01 M sodium acetate and 0.22 M potassium chloride pH 4.6, vapor diffusion, temperature 290K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection twin |
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Reflection | Resolution: 1.8→64.8 Å / Num. all: 42809 / Num. obs: 42809 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Rmerge(I) obs: 0.08 | ||||||||||||||||||
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.45 / % possible all: 100 |
-Phasing
Phasing | Method: MAD |
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-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.8→196.19 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.951 / Occupancy max: 1 / Occupancy min: 1 / SU B: 1.422 / SU ML: 0.046 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.021 / ESU R Free: 0.02 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 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: 449.72 Å2 / Biso mean: 25.0569 Å2 / Biso min: 5.81 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→196.19 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.799→1.846 Å / Total num. of bins used: 20
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