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Yorodumi- PDB-1xo0: High resolution structure of the holliday junction intermediate i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1xo0 | ||||||
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Title | High resolution structure of the holliday junction intermediate in cre-loxp site-specific recombination | ||||||
Components |
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Keywords | HYDROLASE / LIGASE/DNA / CRE RECOMBINASE / HOLLIDAY JUNCTION / RECOMBINATION / COMPLEX (RECOMBINASE-DNA) / LIGASE-DNA COMPLEX | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Enterobacteria phage P1 (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Ghosh, K. / Lau, C.K. / Guo, F. / Segall, A.M. / Van Duyne, G.D. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2005 Title: Peptide trapping of the Holliday junction intermediate in Cre-loxP site-specific recombination. Authors: Ghosh, K. / Lau, C.K. / Guo, F. / Segall, A.M. / Van Duyne, G.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1xo0.cif.gz | 187.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1xo0.ent.gz | 146 KB | Display | PDB format |
PDBx/mmJSON format | 1xo0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xo/1xo0 ftp://data.pdbj.org/pub/pdb/validation_reports/xo/1xo0 | HTTPS FTP |
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-Related structure data
Related structure data | 1xnsC 1crxS C: citing same article (ref.) S: Starting model for refinement |
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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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Details | THE BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE MOLECULE IS A TETRAMER. |
-Components
#1: DNA chain | Mass: 10774.979 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: PART OF HOLLIDAY JUNCTION | ||
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#2: DNA chain | Mass: 10743.969 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: PART OF HOLLIDAY JUNCTION | ||
#3: Protein | Mass: 36549.832 Da / Num. of mol.: 2 / Mutation: R173K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage P1 (virus) / Genus: P1-like viruses / Gene: CRE / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P06956 #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: 3.14 Å3/Da / Density % sol: 50 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 20mM ACETATE BUFFER PH 5.0 40%MPD 20mM CACL2. , VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9188 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD |
Radiation | Monochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9188 Å / Relative weight: 1 |
Reflection | Resolution: 2→26 Å / Num. all: 67741 / Num. obs: 58491 / % possible obs: 96.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Rsym value: 0.076 |
Reflection shell | Resolution: 2→2.09 Å / Num. unique all: 3025 / % possible all: 84.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1CRX Resolution: 2→26 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber Details: The following bond distances are slightly long: peptide bond between chain B residues THR 202 and B LEU 203. phospho diester bridge between chain C nucleotides T 1 and A 2. phospho diester ...Details: The following bond distances are slightly long: peptide bond between chain B residues THR 202 and B LEU 203. phospho diester bridge between chain C nucleotides T 1 and A 2. phospho diester bridge between chain D nucleotides T 1 and A 2.
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Refinement step | Cycle: LAST / Resolution: 2→26 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.09 Å |