+Open data
-Basic information
Entry | Database: PDB / ID: 3c94 | ||||||
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Title | ExoI/SSB-Ct complex | ||||||
Components |
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Keywords | HYDROLASE / Exonuclease / SSB / genome maintenance / DNA damage / DNA repair / DNA replication / DNA-binding / Phosphoprotein | ||||||
Function / homology | Function and homology information single-stranded DNA-binding protein complex / exodeoxyribonuclease I / single-stranded DNA 3'-5' DNA exonuclease activity / nucleoid / DNA catabolic process / replisome / recombinational repair / positive regulation of catalytic activity / SOS response / 5'-deoxyribose-5-phosphate lyase activity ...single-stranded DNA-binding protein complex / exodeoxyribonuclease I / single-stranded DNA 3'-5' DNA exonuclease activity / nucleoid / DNA catabolic process / replisome / recombinational repair / positive regulation of catalytic activity / SOS response / 5'-deoxyribose-5-phosphate lyase activity / mismatch repair / enzyme activator activity / DNA-templated DNA replication / single-stranded DNA binding / 3'-5'-RNA exonuclease activity / DNA recombination / DNA replication / DNA repair / magnesium ion binding / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 Å | ||||||
Authors | Lu, D. / Keck, J.L. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2008 Title: Structural basis of Escherichia coli single-stranded DNA-binding protein stimulation of exonuclease I. Authors: Lu, D. / Keck, J.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3c94.cif.gz | 108.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3c94.ent.gz | 82.6 KB | Display | PDB format |
PDBx/mmJSON format | 3c94.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3c94_validation.pdf.gz | 445.8 KB | Display | wwPDB validaton report |
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Full document | 3c94_full_validation.pdf.gz | 450.9 KB | Display | |
Data in XML | 3c94_validation.xml.gz | 18.4 KB | Display | |
Data in CIF | 3c94_validation.cif.gz | 24.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c9/3c94 ftp://data.pdbj.org/pub/pdb/validation_reports/c9/3c94 | HTTPS FTP |
-Related structure data
Related structure data | 3c95C 1fxxS 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: 55510.566 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: sbcB, cpeA, xonA / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: P04995, exodeoxyribonuclease I | ||||
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#2: Protein/peptide | Mass: 1300.392 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: Peptide was chemically synthesized. The sequence is found naturally in E. coli. References: UniProt: P0AGE0, UniProt: A0A0H3GL04*PLUS #3: Chemical | #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: 2.47 Å3/Da / Density % sol: 50.12 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 18-27% PEG4000, 0.1-0.15M MgCl(2), 0.1 M Tris-HCl; 2:1 ratio of SSB-Ct peptide:exonuclease U, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 3, 2006 |
Radiation | Monochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→20 Å / Num. all: 16401 / Num. obs: 16073 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.079 / Χ2: 2.207 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.383 / Num. unique all: 1412 / Χ2: 1.466 / % possible all: 88.2 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1FXX Resolution: 2.7→20 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.896 / SU B: 26.665 / SU ML: 0.247 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.348 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.763 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.769 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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