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Yorodumi- PDB-8tfu: Structure of Red beta C-terminal domain in complex with SSB C-ter... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8tfu | ||||||
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Title | Structure of Red beta C-terminal domain in complex with SSB C-terminal peptide, Form 1 | ||||||
Components |
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Keywords | DNA BINDING PROTEIN / Recombination / Recombineering / Single Strand Annealing / Single-stranded DNA binding protein / genome engineering | ||||||
Function / homology | Function and homology information nucleoid / single-stranded DNA binding / DNA recombination / DNA replication / DNA repair / DNA binding Similarity search - Function | ||||||
Biological species | Escherichia phage Lambda (virus) Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.482 Å | ||||||
Authors | Bell, C.E. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Mol.Biol. / Year: 2024 Title: Structural Basis for the Interaction of Red beta Single-Strand Annealing Protein with Escherichia coli Single-Stranded DNA-Binding Protein. Authors: Zakharova, K. / Liu, M. / Greenwald, J.R. / Caldwell, B.C. / Qi, Z. / Wysocki, V.H. / Bell, C.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8tfu.cif.gz | 51.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8tfu.ent.gz | 33.6 KB | Display | PDB format |
PDBx/mmJSON format | 8tfu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8tfu_validation.pdf.gz | 441.1 KB | Display | wwPDB validaton report |
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Full document | 8tfu_full_validation.pdf.gz | 441.3 KB | Display | |
Data in XML | 8tfu_validation.xml.gz | 9.5 KB | Display | |
Data in CIF | 8tfu_validation.cif.gz | 13 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tf/8tfu ftp://data.pdbj.org/pub/pdb/validation_reports/tf/8tfu | HTTPS FTP |
-Related structure data
Related structure data | 8tg7C 8tg8C 8tgcC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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: 9428.625 Da / Num. of mol.: 2 / Mutation: GSHM Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia phage Lambda (virus) / Gene: bet, betA, red-beta, redB / Plasmid: pET28b / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): AI / References: UniProt: P03698 #2: Protein/peptide | Mass: 1300.392 Da / Num. of mol.: 2 / Fragment: C-terminal peptide / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli) / References: UniProt: P28044 #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: 2.13 Å3/Da / Density % sol: 42.29 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: 0.48 M sodium phosphate monobasic monohydrate, 1.2 M potassium phosphate dibasic |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 5, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.48→35.444 Å / Num. obs: 25018 / % possible obs: 80.1 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 14.1 |
Reflection shell | Resolution: 1.48→1.59 Å / Redundancy: 6.1 % / Rmerge(I) obs: 1.217 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 1251 / CC1/2: 0.409 / Rpim(I) all: 0.526 / Rrim(I) all: 1.33 / % possible all: 21.2 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.482→34.149 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.003 / SU ML: 0.068 / Cross valid method: FREE R-VALUE / ESU R: 0.082 / ESU R Free: 0.087 Details: Hydrogens have been added in their 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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.448 Å2
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Refinement step | Cycle: LAST / Resolution: 1.482→34.149 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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