[English] 日本語
Yorodumi- PDB-8tg8: Structure of Red beta C-terminal domain in complex with SSB C-ter... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8tg8 | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of Red beta C-terminal domain in complex with SSB C-terminal peptide, Form 3 | ||||||
Components |
| ||||||
Keywords | DNA BINDING PROTEIN / Recombination / Recombineering / Single Strand Annealing / Single-stranded DNA binding protein / genome engineering | ||||||
Function / homology | Bacteriophage lambda, Recombination protein bet / RecT family / RecT family / DNA recombination / DNA binding / Recombination protein bet Function and homology information | ||||||
Biological species | Escherichia phage Lambda (virus) Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.576 Å | ||||||
Authors | Bell, C.E. | ||||||
Funding support | United States, 1items
| ||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8tg8.cif.gz | 32.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8tg8.ent.gz | 18.7 KB | Display | PDB format |
PDBx/mmJSON format | 8tg8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8tg8_validation.pdf.gz | 428.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8tg8_full_validation.pdf.gz | 428.9 KB | Display | |
Data in XML | 8tg8_validation.xml.gz | 5.7 KB | Display | |
Data in CIF | 8tg8_validation.cif.gz | 7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tg/8tg8 ftp://data.pdbj.org/pub/pdb/validation_reports/tg/8tg8 | HTTPS FTP |
-Related structure data
Related structure data | 8tfuC 8tg7C 8tgcC C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 9428.625 Da / Num. of mol.: 1 / Mutation: N-terminal GSHM Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia phage Lambda (virus) / Gene: bet, betA, red-beta, redB / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): AI / References: UniProt: P03698 |
---|---|
#2: Protein/peptide | Mass: 1300.392 Da / Num. of mol.: 1 / Mutation: N-terminal Trp addded / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli) |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 43.97 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.6 Details: 1.2 M sodium citrate tribasic dihydrate, 0.1 M Tris pH 8.6 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
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 / Details: KB mirrors, fixed focus |
Radiation | Monochromator: Kohzu HLD-15 Double Crystal cryocooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.576→49.527 Å / Num. obs: 11588 / % possible obs: 84.6 % / Redundancy: 12.3 % / CC1/2: 1 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.016 / Rrim(I) all: 0.056 / Net I/σ(I): 18.8 |
Reflection shell | Resolution: 1.576→1.683 Å / Redundancy: 11.8 % / Rmerge(I) obs: 2.123 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 580 / CC1/2: 0.473 / Rpim(I) all: 0.615 / Rrim(I) all: 2.213 / % possible all: 24.3 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.576→49.527 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.958 / SU B: 2.388 / SU ML: 0.08 / Cross valid method: FREE R-VALUE / ESU R: 0.095 / ESU R Free: 0.096 Details: Hydrogens have been added in their riding positions
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 44.204 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.576→49.527 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
|